sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
b10b2c9e44ac40cbf67b44fa20a91de553d3ac23262c8d61bd48922045f64898 | MATLAB | 127,689 | 821 | function [Labels] = gretna_label(Template_name)
%==========================================================================
% This function is used to output regional information in different brain
% parcellation atlases.
%
%
% Syntax: function [Labels] = gretna_label(Template_name)
%
% Input:
% Template_name:
% ... |
b05c1eeff9d6aba4197a1ce6280a03fc703bb479b90efc1175ac48a968f3e140 | MATLAB | 130,722 | 2,781 | %% Script for the detection and analysis of oxygen dynamics in the mouse barrel cortex
% Provisional title: Optical investigation of oxygen dynamics in the murine cortex
% Each data folder (e.g 'Recording1') should contain ONLY one tif stack of original motion corrected data and one tif stack of denoised data.
%... |
520e7f7514401498f708c9e12f20edb455586c94900a8f8ed44f04dbb545db0e | MATLAB | 131,943 | 2,833 | %% Script for the detection and analysis of iOS dynamics in the mouse barrel cortex
% This is a modified version of the Oxygen Dynamics analysis
% Provisional title: Optical investigation of oxygen dynamics in the murine cortex
% Each data folder (e.g 'Recording1') should contain ONLY one tif stack of original ... |
a04e5cc36f6619102a90a96f58e70d89ae8f34aed17cd53960478f531c052941 | MATLAB | 145,956 | 3,326 | miceopt = {'Galilei','Haydn','Jemison','Faraday','Lully'};%%options for mice
MouseID = [1,2,3,5,7]; % ID in paper
GenOpt = {'Drd2','Drd1','Drd2','Drd2','Drd1'};%
LocalFolder = '\Path\To\Data\'
ServerDir = '\Path\To\Server'
traininglogdir = '\Path\To\LogFiles\'
Stim2Check = 'SpatialWM' %Name of the stimulus as written i... |
1a040dc4cf68533ab708d76252c3b2c38498c9fa11f0cd9b66861b990973bcfd | MATLAB | 146,819 | 3,473 | % The "qmri-ald" program provides automated image-processing pipelines for
% structural MRI images primarily acquired in pediatric healthy controls
% and pediatric patients with cerebral adrenoleukodystrophy. The program
% provides preprocessing, processing, quantitative, and statistical analysis
% of MRI images such a... |
e1778380094dac5cdfbe30079c17a7ab625005f632c55c0af3f610f258c26217 | MATLAB | 156,504 | 3,508 | % Uses bootstrap to calculate confidence intervals (and p-values) for the
% regression coefficients from a linear model and performs N-way ANOVA.
%
% -- Function File: bootlm (Y, X)
% -- Function File: bootlm (Y, GROUP)
% -- Function File: bootlm (Y, GROUP, ..., NAME, VALUE)
% -- Function File: bootlm (Y, GROUP, ..., '... |
e95b0b4dd135978949c1812938751c4c60e9c219b7ace2a092fec31973222644 | MATLAB | 156,609 | 3,509 | % Uses bootstrap to calculate confidence intervals (and p-values) for the
% regression coefficients from a linear model and performs N-way ANOVA.
%
% -- Function File: bootlm (Y, X)
% -- Function File: bootlm (Y, GROUP)
% -- Function File: bootlm (Y, GROUP, ..., NAME, VALUE)
% -- Function File: bootlm (Y, GROUP, ..., '... |
58fabe0d550632576cb68abd28943272c9a230a5494ad5aa52063d3f28640f9e | MATLAB | 160,086 | 3,156 | function varargout = plot2svg(param1,id,pixelfiletype)
% Matlab to SVG converter
% Prelinary version supporting 3D plots as well
%
% Usage: plot2svg(filename,graphic handle,pixelfiletype)
% optional optional optional
% or
%
% plot2svg(figuresize,graphic handle,pixelfiletype)
... |
19bbe7ba1ccc621557c85c4cd49f4283cc8e0d3d449e8c37c00801ee67a61c46 | MATLAB | 160,454 | 3,094 | function [imageData, alpha] = export_fig(varargin) %#ok<*STRCL1,*DATST,*TNOW1>
%EXPORT_FIG Exports figures in a publication-quality format
%
% Examples:
% imageData = export_fig
% [imageData, alpha] = export_fig
% export_fig filename
% export_fig ... -<format>
% export_fig ... -nocrop
% export_fig ... -c[<... |
f5fbcad5986751029ada4c6ab4750276c8bd5ee445b7a3ca647686c2386379df | MATLAB | 183,010 | 3,985 | %% Script for the statistical analysis of oxygen dynamics as detected by the OxygenDynamics_Master script
% The oxygen sinks need to be manually curated using the
% OxygenDynamics_Sinks_Curation app.
%What does the script do?
% It reads the same csv file as the OxygenDynamics Wrapper containing paths and metadat... |
8754ac9b5604f11462dcca988ec36970fd624f956e8659a2a3a89285e3b7739c | MATLAB | 183,651 | 4,687 | function varargout = TrippleColorMultiChannel_VideoSync_20230506(varargin)
% TRIPPLECOLORMULTICHANNEL_VIDEOSYNC_20230506 MATLAB code for TrippleColorMultiChannel_VideoSync_20230506.fig
% TRIPPLECOLORMULTICHANNEL_VIDEOSYNC_20230506, by itself, creates a new TRIPPLECOLORMULTICHANNEL_VIDEOSYNC_20230506 or raises the ... |
d95070097420a6e2f382e087089dd152f8edb1cab1bb39b98720e43ee6eb0cf3 | MATLAB | 189,506 | 4,875 | classdef Experiment2 < network_project_superclass2
% Class instance for a unique physical coupled learning network.
%% Properties
properties (Constant)
ObjName = 'experiment';
SaveFolder = network_project_superclass2.ExperimentFolder;
end
properties (SetA... |
3fcc3777bbf91a71eac553beae9d8fbd91aeaeafd68e4430e9fa2113c83e39b2 | MATLAB | 200,000 | 4,536 | % RIPPLELAB Multi Analysis EEG Project
% Assisted tool for classification of HFO Events
% Description:
% A computing platform for processing continuous local field potentials
% (LFP). The interface, additional to implement different documented
% algorithms for HFO detection, it provides several tools for ... |
45a29cf6fef65653dde12f23839304126013c4cc3469cb37e3589f69fd4b674d | MATLAB | 200,000 | 790 | function [coef] = read_ctf_coef
% READ_CTF_COEF returns the spatial filter coefficients for the CTF MEG system
% that has been installed at the F.C. Donders Centre (id 1706)
%
% This function actually does not read the coefficients from a file, but the
% coefficients themselves are included in this function.
%
% The ... |
ae9828a3f917bbcd5e67e33c5766fc2c2df2c708e0f8f569e6e854e65c49d2ca | MATLAB | 200,000 | 6,366 | function aedes(DATA,ROI,inputOverlay)
% AEDES - Graphical user interface for analyzing MRI images
%
%
% Synopsis:
% aedes(InArg)
%
% or
%
% aedes
%
% Description:
% AEDES is a graphic user interface (GUI) based tool for region
% of interest (ROI) analysis of (mainly) MRI images.... |
558c2446a2c2de4af2b3cbcd4c3efd54229099219aa01df5219f8b82e1e85f76 | MATLAB | 200,002 | 4,048 | function [HDR,H1,h2] = sopen(arg1,PERMISSION,CHAN,MODE,arg5,arg6)
% SOPEN opens signal files for reading and writing and returns
% the header information. Many different data formats are supported.
%
% Reading of data:
% HDR = sopen(Filename, 'r', [, CHAN [, MODE]]);
% [S,HDR] = sread(HDR, NoR, StartPos);
% ... |
02d65f889b33e9efe5f2d27b505bede4e1c93e5c6ebf6131864a5fadd0c3db25 | MATLAB | 200,016 | 4,259 | classdef eventerapp_exported < matlab.apps.AppBase
% Properties that correspond to app components
properties (Access = public)
Eventer matlab.ui.Figure
CreditsButton matlab.ui.control.Button
StorePanel matlab.ui.container.Panel
UnsavedL... |
5151b882c45914b261228c2c8483fcc01e3bdf566cc7283bbe4d1ff44c40e7cc | Mathematica | 200,000 | 4,122 | (* Content-type: application/vnd.wolfram.mathematica *)
(*** Wolfram Notebook File ***)
(* http://www.wolfram.com/nb *)
(* CreatedBy='Mathematica 12.3' *)
(*CacheID: 234*)
(* Internal cache information:
NotebookFileLineBreakTest
NotebookFileLineBreakTest
NotebookDataPosition[ 158, 7]
Noteb... |
aedf03a67681df11b21a7bc5fc69f02197b9c4d504075d98684b74325e12fe42 | Mathematica | 200,000 | 5,862 | (* Content-type: application/vnd.wolfram.mathematica *)
(*** Wolfram Notebook File ***)
(* http://www.wolfram.com/nb *)
(* CreatedBy='Mathematica 12.2' *)
(*CacheID: 234*)
(* Internal cache information:
NotebookFileLineBreakTest
NotebookFileLineBreakTest
NotebookDataPosition[ 158, 7]
NotebookDataLengt... |
3865d1feeed30547201f6871e6e6c126976e2aeab8883f2688abcb842f508f0a | NEURON | 431 | 22 | GFORTRAN module version '9' created from H5Off_F90.f90
MD5:60dc13016b66ac3d7d67dabceed19421 -- If you edit this, you'll get what you deserve.
(() () () () () () () () () () () () () () () () () () () () () () () ()
() () ())
()
()
()
()
()
(2 'h5o_provisional' 'h5o_provisional' '' 1 ((MODULE UNKNOWN-INTENT
UNKNO... |
61d72b1576be6be3334165a4334b025ac4ad5e54ccb6a12d013b6d618e65d613 | NEURON | 431 | 22 | GFORTRAN module version '9' created from H5Lff_F90.f90
MD5:f973aabb7aec2735ed464a7a283dbe71 -- If you edit this, you'll get what you deserve.
(() () () () () () () () () () () () () () () () () () () () () () () ()
() () ())
()
()
()
()
()
(2 'h5l_provisional' 'h5l_provisional' '' 1 ((MODULE UNKNOWN-INTENT
UNKNO... |
bd8152b76e2ef11c60daf857b9c7d98d4bbc94a8b96cee7721201d23d2fa2ba7 | NEURON | 431 | 22 | GFORTRAN module version '9' created from H5Tff_F90.f90
MD5:0662235e3b0c2a970a275ae4d93e95dc -- If you edit this, you'll get what you deserve.
(() () () () () () () () () () () () () () () () () () () () () () () ()
() () ())
()
()
()
()
()
(2 'h5t_provisional' 'h5t_provisional' '' 1 ((MODULE UNKNOWN-INTENT
UNKNO... |
bfb297c013c002b7637469fe49b767368125134ac2e4c5e970f1b3169bbc3456 | NEURON | 437 | 22 | GFORTRAN module version '9' created from H5_ff_F90.f90
MD5:e546d1f4aee18ce0d6f29c28e9d5cfd1 -- If you edit this, you'll get what you deserve.
(() () () () () () () () () () () () () () () () () () () () () () () ()
() () ())
()
()
()
()
()
(2 'h5lib_provisional' 'h5lib_provisional' '' 1 ((MODULE UNKNOWN-INTENT
U... |
97afc489a8b45f307e066ba8eb7db8137f251a4127d8a7ca4c80bb8a7e4391b3 | NEURON | 2,491 | 53 | module go_ml4h
go 1.20
require (
cloud.google.com/go v0.110.0 // indirect
cloud.google.com/go/bigquery v1.51.2 // indirect
cloud.google.com/go/compute v1.19.0 // indirect
cloud.google.com/go/compute/metadata v0.2.3 // indirect
cloud.google.com/go/iam v0.13.0 // indirect
cloud.google.com/go/storage v1.29.0 // in... |
6d9ae46074e8834f68646caf127e149446cddda617d50c29453da9f76452c73e | NEURON | 3,179 | 63 | module main
go 1.18
require (
github.com/emer/etable v1.0.42
github.com/goki/gi v1.2.18-0.20220729010345-9de4071f7e0d
github.com/goki/ki v1.1.8
github.com/goki/mat32 v1.0.12
)
require (
github.com/BurntSushi/freetype-go v0.0.0-20160129220410-b763ddbfe298 // indirect
github.com/BurntSushi/graphics-go v0.0.0-201... |
a270a8dec140459c48b076062df1841edcc013694b4862f5e4f72540b7dbd208 | NEURON | 4,801 | 87 | GFORTRAN module version '9' created from H5fortran_types.f90
MD5:bb5ca6a494c3015e5e42eccccccfb95b -- If you edit this, you'll get what you deserve.
(() () () () () () () () () () () () () () () () () () () () () () () ()
() () ())
()
()
()
()
()
(2 '__convert_i4_i8' '(intrinsic)' '' 1 ((PROCEDURE UNKNOWN-INTENT
... |
b59177a4cdf028dd7fe1993afdb03b5607fd39831b839f9a764717b4896a1cb7 | NEURON | 127,486 | 2,035 | GFORTRAN module version '9' created from H5f90global.f90
MD5:8ec99fee927bf515522eccebdf8f9bd9 -- If you edit this, you'll get what you deserve.
(() () () () () () () () () () () () () () () () () () () () () () ()
() () () ())
()
(('hdset_reg_ref_t_f' 'h5global' 2) ('hobj_ref_t_f' 'h5global' 3))
(('floating_types' ... |
7e1a3d60358d3b269114a1cc0edfe42930eb73b542996840680f5544fa2dc07a | NEURON | 127,678 | 2,038 | GFORTRAN module version '9' created from H5Fff_F90.f90
MD5:642ea42dd2f0730f5a080c5eb2e5eb60 -- If you edit this, you'll get what you deserve.
(() () () () () () () () () () () () () () () () () () () () () () ()
() () () ())
()
(('hobj_ref_t_f' 'h5global' 2) ('hdset_reg_ref_t_f' 'h5global' 3))
(('floating_types' 4 ... |
73c35b412461f6ac6991f62abf5425056e5cfa0d29f23d3510076c03714aa3cb | NEURON | 128,143 | 2,045 | GFORTRAN module version '9' created from H5Eff_F90.f90
MD5:f7129dabd001d19e7e64963c20dfc9aa -- If you edit this, you'll get what you deserve.
(() () () () () () () () () () () () () () () () () () () () () () ()
() () () ())
()
(('hobj_ref_t_f' 'h5global' 2) ('hdset_reg_ref_t_f' 'h5global' 3))
(('floating_types' 4 ... |
a2ddff50f1e27f1a1acbff125aba63f5e68ac3584289b4956169d91c6ed267d1 | NEURON | 128,420 | 2,050 | GFORTRAN module version '9' created from H5Rff.f90
MD5:dd53f5357d6d87ad7d3d5f9c1f9ace56 -- If you edit this, you'll get what you deserve.
(() () () () () () () () () () () () () () () () () () () () () () ()
() () () ())
()
(('h5rget_object_type_f' 'h5r' 2) ('hobj_ref_t_f' 'h5global' 3) (
'hdset_reg_ref_t_f' 'h5glob... |
f444236d4b7b89ada4c9e7b6c37e37cfa3f37f58bfb7d487c7991bc22dc6abce | NEURON | 130,332 | 2,080 | GFORTRAN module version '9' created from H5Eff.f90
MD5:26c226089cdb07c06c758581b9c62ec2 -- If you edit this, you'll get what you deserve.
(() () () () () () () () () () () () () () () () () () () () () () ()
() () () ())
()
(('hobj_ref_t_f' 'h5global' 2) ('hdset_reg_ref_t_f' 'h5global' 3))
(('floating_types' 4 0 0 ... |
6bb4b20979324801a0458879656c5502d3f5cb13f2c8066b2456f3e9c5aecbdb | NEURON | 131,166 | 2,095 | GFORTRAN module version '9' created from H5_ff.f90
MD5:449e50eaef035b238eddfd5111950f2e -- If you edit this, you'll get what you deserve.
(() () () () () () () () () () () () () () () () () () () () () () ()
() () () ())
()
(('hobj_ref_t_f' 'h5global' 2) ('hdset_reg_ref_t_f' 'h5global' 3))
(('floating_types' 4 0 0 ... |
c6c5f61186bbbb4108e8db4600371a21de02c929f90866adb0a12876712d47f0 | NEURON | 132,031 | 2,106 | GFORTRAN module version '9' created from H5Iff.f90
MD5:4a307fa50f1718c1d05d206f8eed4efc -- If you edit this, you'll get what you deserve.
(() () () () () () () () () () () () () () () () () () () () () () ()
() () () ())
()
(('hobj_ref_t_f' 'h5global' 2) ('hdset_reg_ref_t_f' 'h5global' 3))
(('floating_types' 4 0 0 ... |
75694e877746877c7d8f8619670cd883c330ba59caedf46791f7835722d08013 | NEURON | 133,623 | 2,131 | GFORTRAN module version '9' created from H5Rff_F90.f90
MD5:04a149517f485f6bcd2d18873e7031cc -- If you edit this, you'll get what you deserve.
(() () () () () () () () () () () () () () () () () () () () () () ()
() () () ())
()
(('h5rcreate_f' 'h5r_provisional' 2 3) ('h5rdereference_f'
'h5r_provisional' 4 5) ('h5rge... |
0c5d11e9a2507e8509c9f23f099641508e896ea8f0f0cc666c32edfa0c1a7121 | NEURON | 138,241 | 2,200 | GFORTRAN module version '9' created from H5Fff.f90
MD5:686011f8ab105405253b740fa7b0893c -- If you edit this, you'll get what you deserve.
(() () () () () () () () () () () () () () () () () () () () () () ()
() () () ())
()
(('hobj_ref_t_f' 'h5global' 2) ('hdset_reg_ref_t_f' 'h5global' 3))
(('floating_types' 4 0 0 ... |
fdb75477353c53c766c8d7adf276ca54e254797ddb3cedbe2a5d54ccc21a8d41 | NEURON | 138,401 | 2,199 | GFORTRAN module version '9' created from H5Off.f90
MD5:9714ce2d1a496bc7c51b7fef271207e6 -- If you edit this, you'll get what you deserve.
(() () () () () () () () () () () () () () () () () () () () () () ()
() () () ())
()
(('hobj_ref_t_f' 'h5global' 2) ('hdset_reg_ref_t_f' 'h5global' 3))
(('floating_types' 4 0 0 ... |
abe78d16864a8eb1955cf5dfd426df1277fca0dc91963784422719d49cbde5a5 | NEURON | 141,968 | 2,248 | GFORTRAN module version '9' created from H5Lff.f90
MD5:ff5a9c648a6a297e896b72997081adf9 -- If you edit this, you'll get what you deserve.
(() () () () () () () () () () () () () () () () () () () () () () ()
() () () ())
()
(('hobj_ref_t_f' 'h5global' 2) ('hdset_reg_ref_t_f' 'h5global' 3))
(('floating_types' 4 0 0 ... |
a5234a8d30aca7588c9421bc18ece087011d30fec96520ef82c4dce03af58cb5 | NEURON | 143,071 | 2,273 | GFORTRAN module version '9' created from H5Pff_F90.f90
MD5:c4be90312c6d3d2bd28987f1428ca48d -- If you edit this, you'll get what you deserve.
(() () () () () () () () () () () () () () () () () () () () () () ()
() () () ())
()
(('h5pget_fill_value_f' 'h5p_provisional' 2 3 4) ('h5pget_f'
'h5p_provisional' 5 6 7) ('h... |
1ae6ab860db0fcf87a9467923d75a1176cc818cf1cdfbfc2f43f8fd32d4ba774 | NEURON | 144,324 | 2,290 | GFORTRAN module version '9' created from H5Gff.f90
MD5:f6cc45b3c8adec167633b347a291f061 -- If you edit this, you'll get what you deserve.
(() () () () () () () () () () () () () () () () () () () () () () ()
() () () ())
()
(('hobj_ref_t_f' 'h5global' 2) ('hdset_reg_ref_t_f' 'h5global' 3))
(('floating_types' 4 0 0 ... |
177a974ef1115df3ac9b5975f61032f8730e9b23ec228ad11e3661e5f94bcaa8 | NEURON | 148,197 | 2,355 | GFORTRAN module version '9' created from H5Sff.f90
MD5:4a8a423818279c5e3c3f0c9fdd80a883 -- If you edit this, you'll get what you deserve.
(() () () () () () () () () () () () () () () () () () () () () () ()
() () () ())
()
(('hobj_ref_t_f' 'h5global' 2) ('hdset_reg_ref_t_f' 'h5global' 3))
(('floating_types' 4 0 0 ... |
39c05d489373c48ac423ff02406f01a9503dc9708719cbb3a06729fe03e376de | NEURON | 148,649 | 2,365 | GFORTRAN module version '9' created from H5Dff.f90
MD5:6613180d604b2c342ace1664bbad2a46 -- If you edit this, you'll get what you deserve.
(() () () () () () () () () () () () () () () () () () () () () () ()
() () () ())
()
(('h5dextend_f' 'h5d' 2) ('h5dread_vl_f' 'h5d' 3 4 5) ('h5dwrite_vl_f'
'h5d' 6 7 8) ('hobj_re... |
8650eae0fb51627dd8ed7f3348de48b9c78567a0988f8ad743a0e70373956fa5 | NEURON | 151,650 | 2,401 | GFORTRAN module version '9' created from H5Aff.f90
MD5:5cee0fdc4485cf25398e7739f492e3dd -- If you edit this, you'll get what you deserve.
(() () () () () () () () () () () () () () () () () () () () () () ()
() () () ())
()
(('hobj_ref_t_f' 'h5global' 2) ('hdset_reg_ref_t_f' 'h5global' 3))
(('floating_types' 4 0 0 ... |
e35173168844ff4b792fc260d6465f4ae3e4dd57745d89b6b6d7fa44d333d21a | NEURON | 167,905 | 2,664 | GFORTRAN module version '9' created from H5Tff.f90
MD5:2da854c8d347ec3a2b8b5d409a126701 -- If you edit this, you'll get what you deserve.
(() () () () () () () () () () () () () () () () () () () () () () ()
() () () ())
()
(('hobj_ref_t_f' 'h5global' 2) ('hdset_reg_ref_t_f' 'h5global' 3))
(('floating_types' 4 0 0 ... |
92009e68eafa7a52787ba96f5adb3c86de20b8407ee0550f8354ba332dab88d3 | NEURON | 190,649 | 3,007 | GFORTRAN module version '9' created from H5_DBLE_InterfaceInclude.f90
MD5:6b73523191587da7a9b8e1eee42e071f -- If you edit this, you'll get what you deserve.
(() () () () () () () () () () () () () () () () () () () () () () ()
() () () ())
()
(('h5aread_f' 'h5_dble_interface' 2 3 4 5 6 7 8 9) ('h5awrite_f'
'h5_dble_... |
136b105c96ec9b2a905eb5f3f8aab68254fc7556034ad3b7f80626f6c22122ca | NEURON | 200,000 | 3,116 | GFORTRAN module version '9' created from H5Aff_F90.f90
MD5:a5eca7043d280592ee070380a0dcd087 -- If you edit this, you'll get what you deserve.
(() () () () () () () () () () () () () () () () () () () () () () ()
() () () ())
()
(('h5aread_f' 'h5a_provisional' 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17
18 19 20 21 22 23... |
173254403d7d7ea626e021972f6857094e00ee3dd2f3b730a840f8950ffd1062 | NEURON | 200,000 | 2,941 | GFORTRAN module version '9' created from H5TBff.f90
MD5:8ceb8b60b30c1ab3f62b9a1dbc398216 -- If you edit this, you'll get what you deserve.
(() () () () () () () () () () () () () () () () () () () () () () ()
() () () ())
()
(('h5aread_f' 'hdf5' 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21
22 23 24 25 26 27 2... |
717f88b59acf3996967b81387c84978340d0836555eee484f6f766464ee23656 | NEURON | 200,000 | 3,173 | GFORTRAN module version '9' created from H5Dff_F90.f90
MD5:83e3647caf19b935c697629b1d3ae170 -- If you edit this, you'll get what you deserve.
(() () () () () () () () () () () () () () () () () () () () () () ()
() () () ())
()
(('h5dfill_f' 'h5d_provisional' 2 3 4) ('h5dread_f' 'h5d_provisional' 5
6 7 8 9 10 11 12 ... |
87a718881ea0cc8088dac5ff8c38e518748f7aaf1fc00862e7ca6f9b4f67b371 | NEURON | 200,000 | 2,940 | GFORTRAN module version '9' created from H5LTff.f90
MD5:fa263cc6e4a1817308314505af21506b -- If you edit this, you'll get what you deserve.
(() () () () () () () () () () () () () () () () () () () () () () ()
() () () ())
()
(('h5aread_f' 'hdf5' 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21
22 23 24 25 26 27 2... |
ab68095f591bf9e9ca1c4b6fb07553961f69952aa8d243d270324fb3c76ae3a4 | NEURON | 200,000 | 3,161 | GFORTRAN module version '9' created from H5Pff.f90
MD5:bd53f39f53a89a1127644a7d82248b80 -- If you edit this, you'll get what you deserve.
(() () () () () () () () () () () () () () () () () () () () () () ()
() () () ())
()
(('h5pset_fapl_multi_f' 'h5p' 2 3) ('hobj_ref_t_f' 'h5global' 4) (
'hdset_reg_ref_t_f' 'h5glo... |
b3d854ad557ffa19ee8f49b1f6855856cb4d3d879a73068328bc7f2857b3f5f9 | NEURON | 200,000 | 2,940 | GFORTRAN module version '9' created from H5DSff.f90
MD5:aee157f2f446c1632bf862a73e2b09a4 -- If you edit this, you'll get what you deserve.
(() () () () () () () () () () () () () () () () () () () () () () ()
() () () ())
()
(('h5aread_f' 'hdf5' 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21
22 23 24 25 26 27 2... |
e9759d2613d9f9756b11cc0de7d6b3a4c5eb6c47b3642a1a35fadd8e9ff3bb30 | NEURON | 200,000 | 2,940 | GFORTRAN module version '9' created from H5IMff.f90
MD5:6b4ccf944bbc01d56891971aac89e31a -- If you edit this, you'll get what you deserve.
(() () () () () () () () () () () () () () () () () () () () () () ()
() () () ())
()
(('h5aread_f' 'hdf5' 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21
22 23 24 25 26 27 2... |
fe5f077db3f430b3e03c3095a35e4d51ec8bc92a48d2759335ddd2347074dec2 | Perl | 380 | 14 | #!/usr/bin/env perl
# inject separator after all alignment of a read pair
use strict;
use warnings;
my $readname;
while (<>) {
my $original_line = $_;
if (substr($original_line, 0, 1) ne "@") {
my @fields = split("\t", $original_line);
print "__\n" if defined $readname && $readname ne $fields[0];
... |
3d009ffeca677dd3ca235a8caebebca6efd1f751ef92a65ad5aee3dc7cab191d | Perl | 523 | 15 | #!/usr/bin/perl
$die = "
sciMET_addAnnotsToDMRs.pl [DMR bed file with qval & cluster etc] [output file]
Adds columns for Gencode category, Genehancer class
";
if (!defined $ARGV[1]) {die $die};
system("perl /home/users/adey/adey-src/add_annot_to_bed.pl $ARGV[0] /home/groups/ravnica/refs/hg38/hg38.gencode_regions.... |
4b5d9aa04b6400cd48695ba476501abc06acc227a63b59991de5a696ccafd084 | Perl | 532 | 28 | #!/usr/bin/perl
$die = "
sciMET_methylKit2bgph.pl [input methylKit window file] [window size] [min cov] > [out bedgraph]
";
if (!defined $ARGV[2]) {die $die};
open IN, "$ARGV[0]";
$null = <IN>;
#chrBase chr base strand coverage freqC freqT
#chr1.11000 chr1 11000 F 90 35.55 ... |
51745a7306abe652690539a79208b6bf3467483363f1d3912e2433342878ace1 | Perl | 549 | 30 | #!/usr/bin/perl
$die = "
sciMET_mtx2covInfo.pl [cov mtx file] > [output stats on cells]
";
if (!defined $ARGV[0]) {die $die};
open IN, "$ARGV[0]";
$h = <IN>; @H = split(/\t/, $h);
while ($l = <IN>) {
chomp $l;
@P = split(/\t/, $l);
$siteID = shift(@P);
for ($i = 0; $i < @H; $i++) {
if ($P[$i] > 0) {
$CELL... |
6fc08e5d530349060b22e58594619474e1cffee08d3982637a6dbe4e89c48d79 | Perl | 600 | 26 | #!/usr/bin/perl
$die = "
sciMET_aggregate_trim_stats.pl [list of trim stats txt files, min 2] > [aggregated stats by cellID]
";
if (!defined $ARGV[1]) {die $die};
foreach $in (@ARGV) {
open IN, "$in";
while ($l = <IN>) {
chomp $l;
@P = split(/\t/, $l);
$CELLID_total{$P[0]} += $P[1];
$CELLID_retained{$P[0... |
45157cf7971f1e5b331290136f1561176f251befed8753c2df420f047bed42e7 | Perl | 637 | 40 | #!/usr/bin/perl
$die = "
sciMET_compareDMRs.pl [truth bed of DMRs] [bed from collated cluster DMRs]
";
if (!defined $ARGV[1]) {die $die};
open IN, "cat $ARGV[0] $ARGV[1] | awk '{print \$1\"\\t\"\$2\"\\t\"\$3\"\\t\"\$4}' | sortBed | mergeBed -o distinct -c 4 |";
while ($l = <IN>) {
chomp $l;
@P = split(/\t/, $l);... |
7ba2ce239f300e4df7620fd228ba86e2a7daa3bcb71a57a4c415ab30fcc4ca09 | Perl | 638 | 25 | use 5.006;
use strict;
use warnings;
use Module::Build;
my $builder = Module::Build->new(
module_name => 'cworld::dekker',
license => 'perl',
dist_author => q{Bryan R. Lajoie <bryan.lajoie@gmail.com>},
dist_version_from => 'lib/cworld/dekker.pm',
release_status =>... |
4ac3f080a472e7b2afadf38aec03cc0658727825d18dacd2efac669dd25d9728 | Perl | 649 | 27 | #!/usr/bin/perl
use strict;
## Usage filter-peptides.pl FILE SCORE; SCORE is the minimum score
open (FILE, $ARGV[0]) || die "\nError: The file $ARGV[0] does not exist\n\n";
my $prot = "";
my $treshold = 1;
if ($ARGV[1]) {
$treshold = $ARGV[1];
}
while (<FILE>){
next if (/^Position/); #skip the header line
if (/... |
19b0916ad370957378190472ab17018c065d3b910d96fa72f8a60e66cfcc7687 | Perl | 674 | 41 | #!/usr/bin/perl
$die = "
sciMET_find_CAC.pl [genome fasta].gz > [CAC sites bed file]
";
if (!defined $ARGV[0]) {die $die};
if ($ARGV[0] =~ /gz$/) {
open IN, "zcat $ARGV[0] |";
} else {
open IN, "$ARGV[0]";
}
while ($l = <IN>) {
chomp $l;
if ($l =~ /^\>/) {
$pos = 0;
$chr = $l;
$chr =~ s/^\>//;
$chr =~ ... |
3828b75e797f40ee4a66b0c17301a4ce8a311eb4899442ee96bcf059075a2d5a | Perl | 685 | 40 | #!/usr/bin/perl
$die = "
sciMET_find_DCM.pl [genome fasta].gz > [DCM sites bed file]
";
if (!defined $ARGV[0]) {die $die};
if ($ARGV[0] =~ /gz$/) {
open IN, "zcat $ARGV[0] |";
} else {
open IN, "$ARGV[0]";
}
while ($l = <IN>) {
chomp $l;
if ($l =~ /^\>/) {
$pos = 0;
$chr = $l;
$chr =~ s/^\>//;
$chr =~ ... |
5e1cd063b9d791b51e303f7ca2463563547f9ef006699264cf2db4be2a90f380 | Perl | 700 | 35 | #!/usr/bin/perl
#
# tophat_bam_header_revise.pl
#
# xwei 7/6/2013
## add more information to the header of .bam files
## example: perl /home/CAM/xwei/tgchome/script/encode_pipeline/tophat_bam_header_revise.pl /home/CAM/xwei/tgchome/tophatTest_15/YEO_8-16/unmapped.bam
use strict;
use FileHandle;
my $BAM= $ARGV... |
56d176e9f6be9898ac5bdc70f8bc3bb430b5c516a400dae95cf0bd1216a9247d | Perl | 754 | 43 | #!/usr/bin/perl
use strict;
use warnings;
use 5.010;
use List::Util qw[min max];
my $col1;
my $col2;
my $name;
my $chr;
my $start;
my $end;
my $strand;
my $count = 0;
my $spliceSite;
my $firstSeq;
my $len;
my $genomeStrand;
while (<>) {
chomp();
$count++;
($col1, $col2) = split ("\t",$_);
($name, $chr, $start, $... |
acda1aa57bdfaf9b2fe293d39a7f898c004dc05d31a6b44fc4b624712dc8348a | Perl | 768 | 44 | #!/usr/bin/perl
$die = "
sciMET_find_GpCs.pl [genome fasta].gz > [GC sites bed file]
";
if (!defined $ARGV[0]) {die $die};
if ($ARGV[0] =~ /gz$/) {
open IN, "zcat $ARGV[0] |";
} else {
open IN, "$ARGV[0]";
}
while ($l = <IN>) {
chomp $l;
if ($l =~ /^\>/) {
$pos = 0;
$chr = $l;
$chr =~ s/^\>//;
$chr =~ ... |
bf23bc7bf65e53b51e341a975f01292444a242f60c061bd5697d6d9557e6b0e0 | Perl | 769 | 44 | #!/usr/bin/perl
$die = "
sciMET_find_GpCs.pl [genome fasta].gz > [GC sites bed file]
";
if (!defined $ARGV[0]) {die $die};
if ($ARGV[0] =~ /gz$/) {
open IN, "zcat $ARGV[0] |";
} else {
open IN, "$ARGV[0]";
}
while ($l = <IN>) {
chomp $l;
if ($l =~ /^\>/) {
$pos = 0;
$chr = $l;
$chr =~ s/^\>//;
$chr =~ ... |
04dbc764d57a8abcb75de8e06a1ec94848baa49ab3a7cb41b2e4c8d57f3d5c84 | Perl | 818 | 45 | #!/usr/bin/perl
#chr1 870000 872000 noCap.1 0.00736569998486068 -37.5
#chr1 13201 13800 Enhancer
$die = "
sciMET_annotateDMR.pl [bed with classes] [DMRs] > [annotation added to DMR file]
DMR file:
chr start end sample cluster qval methDiff
Out adds: class from bed file or 'None'
";
if (!... |
34f5d6145ae69338882ca60a11dda9bb851f6f4666015efc0f0eaf7122d8a7a6 | Perl | 829 | 36 | #!/usr/bin/perl
$die = "
sciMET_sortChroms.pl [chrom folder] (run)
Wrapper to sort the files in a chroms folder.
Will kick each off simultaneously using as many
threads as there are files.
Wrapper for linx sort command.
Sorts with -k1,1 -k2,2n, gzips and then deletes
original file, replacing it with the sorted one.... |
227e60e0e54aefc5a73c65a9acd60a63e2ea9e88e37ede7c6994c9089309bc53 | Perl | 923 | 40 | #!/usr/bin/perl
$die = "
sciMET_annot_compare.pl [truth annot] [test annot] [outfile]
";
if (!defined $ARGV[2]) {die $die};
open IN, "$ARGV[0]";
while ($l = <IN>) {
chomp $l;
($cellID,$annot) = split(/\t/, $l);
$trueAnnot{$annot} = $annot;
$CELLID_trueAnnot{$cellID} = $annot;
} close IN;
open IN, "$ARGV[1]";
... |
970982ad458583dfef9ba481f40c24080eb954a1b5219988f0083f3a4ac51ba8 | Perl | 923 | 44 | #!/usr/bin/perl
$die = "
sciMET_chroms2bulkMethylKit.pl [input chroms file] > [output methylKit file]
Chrom files must be gzipped and sorted!
";
if (!defined $ARGV[0]) {
die $die;
}
opendir(CHR, "$ARGV[0]");
@CHRS = readdir(CHR);
closedir(CHR);
print "chrBase\tchr\tbase\tstrand\tcoverage\tfreqC\tfreqT\n";
fore... |
03146f0921b2e4ba9b94221ee3d20560ab7da16ccdb1fc1b24b47ecfe81d938c | Perl | 964 | 42 | #!/usr/bin/perl
use strict;
# This program includes or excludes the sequences of a fasta file based on a list of sequences ids given by the user
## Usage filter_fasta.pl FASTA LIST_ID [-e]; FASTA is the fasta file | LIST_ID is the list of ids | -e if you want to EXCLUDE the sequences matching LIST_ID (by default the... |
e918f4dc55a78a371304900f3f4e08356cdbd38ab7e26d5c7d91fc1494fcc108 | Perl | 1,066 | 57 | #!/usr/bin/perl
use strict;
use warnings;
use 5.010;
#use List::Util qw[min max];
my $col1;
my $col2;
my $col3;
my $col4;
my $col5;
my $col6;
my $col7;
my $col8;
my $col9;
my $col10;
my $col11;
my $col12;
my $col13;
my $col14;
my $col15;
my $col16;
my $col17;
my $col18;
my $col19;
my $col20;
my $col21;
my $name;
my @... |
ac7525bb3ccd0348779774981c4634d880a0d9102d9f2d796617530b135f73e1 | Perl | 1,162 | 58 | #!/usr/bin/perl
use strict;
use warnings;
use 5.010;
#use List::Util qw[min max];
my $col1;
my $col2;
my $col3;
my $col4;
my $col5;
my $col6;
my $col7;
my $col8;
my $col9;
my $col10;
my $col11;
my $col12;
my $col13;
my $col14;
my $col15;
my $col16;
my $col17;
my $col18;
my $col19;
my $col20;
my $col21;
my $name;
my @... |
e54df0b74809cfb06202689d7ec1b1eaf681c41b67c830da034e78935297737b | Perl | 1,204 | 49 | #!/usr/bin/perl
#chr10 101288606 66.67 1 2
$die = "
ARGV0 = cellcall folder
ARGV1 = annot of clusters
ARGV2 = out folder
ARGV3 = CG or CH (def = CG)
will generate a bed of sites covered by cluster
";
if (!defined $ARGV[2]) {die $die};
if (defined $ARGV[3]) {$context = $ARGV[3]} else {$context = "... |
bb03ffa38621cbfe556be23ad368682262b34b7c5a755cb9389702c225fb48c8 | Perl | 1,219 | 63 | #!/usr/bin/perl -w
#
# Fasta splitter jepl version
# Splits a fasta file into fasta files, that only contain one sequence.
# The names of the files are given by the number of the sequence.
# Import libraries
#
use Getopt::Std; # Command line options
use strict; # Strict parsing
use English; # Allow use of lo... |
da23c66345b7c76227803679ce88c88aac37d09fece30df3af5f6e87163a6385 | Perl | 1,221 | 51 | #!/usr/bin/perl
$die = "
sciMET_mergeSVD.pl [output matrix] [input matrix ] [input matrix 2] (input matrix N) ...
Merges matrixes, retaining only the union of cells and all rows from
all matrixes. Can be used to merge SVD matrixes from CH and CG contexts.
Appends fileID to the end of the windowID.
";
if (!defined ... |
0e08059bd78f350b983c3edbcde0dc1ec46eab641d17c2dc2fd5f462b1baa558 | Perl | 1,230 | 62 | #!/usr/bin/perl
use strict;
use warnings;
use 5.010;
#use List::Util qw[min max];
my $col1;
my $col2;
my $col3;
my $col4;
my $col5;
my $col6;
my $col7;
my $col8;
my $col9;
my $col10;
my $col11;
my $col12;
my $col13;
my $col14;
my $col15;
my $col16;
my $col17;
my $col18;
my $col19;
my $col20;
my $col21;
my $name;
my @... |
499e75b927b55987b479a052a02544374c69313f09817c01d3399eb1fec0d9b0 | Perl | 1,292 | 40 | #!/usr/bin/perl
use strict;
# This script will merge lines with a shared sequence and report the sequences in fasta format
## Usage filter_dup.pl TAB DUP; TAB is a file that contains IDs and sequences, tab separated. DUP is the file that contains duplicated sequences
my %dups=();
open (FILE, $ARGV[1]) || die "\nEr... |
49071609e0776ff90bc0ad150101fde7c4001f8a26d0f9c799349f1a14f81bab | Perl | 1,360 | 49 | #!/usr/bin/perl
$die = "
ARGV0-N = methylKit files for each cluster
Outputs a file with the same name, but adds NOT before methylKit.txt
this is for each cluster - to be used as a comparison in
methylKit, loading the cluster and the NOT aggregate cells
then performing the DMR analysis
Min cov is set to 10 (hardcoded... |
896f62fdc5953d1cd4ca08397811a7b0ee21c71ec19d61fed809db6a38fc7b84 | Perl | 1,396 | 46 | #!/usr/bin/perl
use strict;
## Usage random_fasta.pl FASTA N TOTAL; N is the number of (random) chosen sequences, TOTAL is the total number of sequences
if ($#ARGV < 2) {
print "This program randomly chooses N sequences from a multifasta file\n\nUsage: random_fasta.pl FILE.fa N TOTAL\n\nFILE.fa\tThe name of your fas... |
2deb49caa61a7c0b659bf00be11a8bb2ea8fe303690a2e2d1049f34b0ac4ae77 | Perl | 1,459 | 58 | #! /usr/bin/perl -w
# ============================================================
use Getopt::Long;
use strict;
use warnings;
# read bed file
# ============================================================
my %bed_start = ();
my %bed_end = ();
my %ref = ();
my %alt = ();
while (<>) {
chomp $_;
my @this_l... |
30e5d6b941908ec7d469899b1a8d07086a37126443872be1340b77da12ec470c | Perl | 1,498 | 80 | #!/usr/bin/perl
=head1 Name
generate_font_width_hash.pl -- generate font width hash for Font.pm
=head1 Description
useful information for each character:
$ref->{defs}{font}{font-face}{font-family}
$ref->{defs}{font}{glyph}[0]{unicode}
$ref->{defs}{font}{glyph}[0]{horiz-adv-x}
$ref->{defs}{font}{horiz-adv-x}
=head... |
5530b9836b12b991c5810541959efb4b34521b263e5907ed801c5185d3d12628 | Perl | 1,527 | 78 | #!/usr/bin/perl -w
# File: faslines.pl
# Author: Sanzhen Liu
# Date: 3/23/2023
use strict;
use warnings;
use Getopt::Long;
my $minlen=0;
my $linelen = 99;
my $outdir = ".";
my $prefix = "";
my $help;
my $result = &GetOptions("minlen|i=i" => \$minlen,
"outdir|o=s" => \$outdir,
"prefix... |
2fb2d0fd6d2190aeb631dfaf0e0adb53908e9dffaadfcd7fec126dc691d839bc | Perl | 1,573 | 58 | #!/usr/bin/perl
use Getopt::Std; %opt = ();
getopts("F:B:O:", \%opt);
$die = "
Usage:
sciMET_filtChroms.pl -F [chromosome meth call folder(s)] -O [output folder] -B [Bed of targets]
Filters chrom folders to only include calls within regions and outputs a single
chroms folder for those calls. Needs to be sorted.
... |
5cfcd7a56105de80bf999fd9528790f0200cdbf7c121d442a4207f944f241793 | Perl | 1,673 | 80 | #!/usr/bin/perl
=head1 Name
generate_font_width_hash.pl -- generate font width hash for Font.pm
=head1 Description
useful information for each character:
$ref->{defs}{font}{font-face}{font-family}
$ref->{defs}{font}{glyph}[0]{unicode}
$ref->{defs}{font}{glyph}[0]{horiz-adv-x}
$ref->{defs}{font}{horiz-adv-x}
=head... |
1cad846a2bdabbea4bd18afe440495fd7db0e89b42ff98c3c0dff90796201b87 | Perl | 1,717 | 65 | #!/usr/bin/perl
use Getopt::Std; %opt = ();
getopts("1:O:q:m:w:n:", \%opt);
$qcut = "0.0001";
$mcut = "25";
$wsize = 1500;
$die = "
sciMET_collateDMRclusters.pl [options] -1 [DMR...pg_1].txt
Options:
-1 [STR] DMR output for cluster 'pg_1' (req)
Must have 'pg_1' as cluster and all other
... |
18d5bbf64b38df7a8423fdfbdc802ebfd77a2429fb8181ccacbbd4b74e1f0df5 | Perl | 1,771 | 76 | #!/usr/bin/perl
use strict;
use warnings;
use 5.010;
#use List::Util qw[min max];
my $col1;
my $col2;
my $col3;
my $col4;
my $col5;
my $col6;
my $col7;
my $col8;
my $col9;
my $col10;
my $col11;
my $col12;
my $col13;
my $col14;
my $col15;
my $col16;
my $col17;
my $col18;
my $col19;
my $col20;
my $col21;
my $name;
my @... |
240244b3cb01f68fe9e9342178c96f129a3ef5f90d417fb9e7cd01dac639a984 | Perl | 1,801 | 78 | #!/usr/bin/perl
$die = "
sciMET_mergeMtx.pl [output name] [matrix 1] [matrix 2] (matrix 3) ...
Must have no overlapping cells unless adding annot. Must be same rows.
Can specify [output annot file],[output matrix] [matrix1 annot],[matrix 1] etc...
This will add the annot ID to the cell name and also
output an annot... |
53b5b763c49ac0c65c75dd351f13bb2cec876a1f5cb53b38bbfe300a91d34173 | Perl | 1,865 | 48 | #!/usr/bin/perl
# Program to filter Wikipedia XML dumps to "clean" text consisting only of lowercase
# letters (a-z, converted from A-Z), and spaces (never consecutive).
# All other characters are converted to spaces. Only text which normally appears
# in the web browser is displayed. Tables are removed. Image capt... |
e69e9b363d60fc4ff4188b1b375bc63fb78a9fc6148eba37648a189eb88f8476 | Perl | 1,875 | 91 | #!/usr/bin/perl
use strict;
use warnings;
use 5.010;
#use List::Util qw[min max];
#use Math::Round;
my $col1;
my $col2;
my $col3;
my $col4;
my $col5;
my $col6;
my $col7;
my $col8;
my $col9;
my $col10;
my $col11;
my $name;
my $first_name = "Morten";
my $first_col2;
my $sum_col5 = 0;
my $sum_col6 = 0;
my $sum_col7 = 0;... |
76429107e194e7730832cbd660a0c0d9f700298d663fb707d46d81a3ca64daeb | Perl | 1,968 | 81 | #!/usr/bin/perl
$die = "
sciMET_perCellAlignRate.pl \
[read 1 AND 2 fastq file(s), post-trim - can be comma separated OR files from trim output on R1 and R2 stats - also comma sep; can be a mix] \
[aligned bam file(s), pre-rmdup OR complexity.txt file(s), can be comma separated an a mix of types] \
[list fo cellID... |
db56b0ad3a6a66b047ce95aeafcc8ff456d429fd5ce8b45975f70916f3ccd2f6 | Perl | 2,015 | 81 | #!/usr/bin/perl
$die = "
sciMET_split_GpC_calls.pl [GpC bed file] [chroms folder in] (chroms folder in 2) ...
Will output two new chroms folders using the input as the
output prefix for each chroms folder.
";
if (!defined $ARGV[1]) {die $die};
open GC, "$ARGV[0]";
while ($l = <GC>) {
chomp $l;
($chrom,$start,$e... |
be86b7047c0e7a39f043d53cf762fe2a9fa8afb58dc163ca1f8c63fe36325705 | Perl | 2,031 | 82 | #!/usr/bin/perl
$die = "
sciMET_BSBolt_StrandBias.pl [myBam] [out prefix] (optional: CellID list)
Generates:
[out].cellStrandBias.txt (per cell)
[out].strandBias.txt (global)
If a text file of cellIDs is provided it will only include information
from those cell IDs in both global and cell-level outputs.
";
if (!... |
73f411288b3b19f9c6d92359fc0e4f6878f6eb7d27d9976af08e313e3d9945e6 | Perl | 2,055 | 73 | #!/usr/bin/perl
use Getopt::Std; %opt = ();
getopts("P:A:m:O:", \%opt);
#defaults
$min = 50;
$die = "
Usage:
sciMET_annotPairwise.pl -P [pairwise file] -A [annot file] -O [output prefix]
Produces all-by-all cell overlap and shared cytosine methylation.
Options:
-P [STR] Pairwise methylation call file (req)
... |
1ecc5ad7f7947cd7ca407bea165b773a3b5455e69008073c8a0f485ec24743b5 | Perl | 2,070 | 87 | #!/usr/bin/perl
use Getopt::Std; %opt = ();
getopts("M:C:O:A:", \%opt);
$die = "
sciMET_mtx2methylKitAnnot.pl -M [methylation percent matrix] -C [coverage matrix] -O [output prefix] -A [cluster annot file]
Gets methylation calls into a format that methylKit can use for DMR detection on a
cluster level.
Options:
... |
d5fd3ca1e5503915e25f5d3aa06e462054f801c5e3a52e0fc8907d89b1083ef5 | Perl | 2,165 | 72 | #!/usr/bin/perl
use Getopt::Std; %opt = ();
getopts("O:A:F:O:", \%opt);
$die = "
sciMET_Annot2methylKit.pl -F [CG methyl call folder] -O [output prefix] -A [cluster annot file]
Gets methylation calls into a format that methylKit can use for DMR detection on a
cluster level.
Options:
-O [STR] Output prefix ... |
8e3c488539414b0f7810c6bb188485ba94603031c3cbb9815de53d05ab49bbfc | Perl | 2,219 | 75 | #!/usr/bin/perl
$die = "
sciMET_cellCall2info.pl [cellCall folder] > [cellInfo output]
Will print CG then CH contexts then any additional contexts
";
if (!defined $ARGV[0]) {die $die};
opendir(CCD, "$ARGV[0]");
@CELLCALLS = readdir(CCD);
closedir(CCD);
$alt = 0;
foreach $cellCall (@CELLCALLS) { if ($cellCall =~ /... |
6103709cdd9f6382e24accdac8c1d0c6ca63b4b17a2d949288370637528195e3 | Perl | 2,465 | 91 | #!/usr/bin/perl -w
#
# ====================================================================================================
# File: fastaSize.pl
# Author: Sanzhen Liu
#
# This file count the size of each sequence in the input file if not specify the option --all.
# If the option --all is added, count the total size of... |
98a993236d4288c4c737e4c3ae4e3aaccb51451cdca73d0808d964dc885ee2d1 | Perl | 2,610 | 117 | #!/usr/bin/perl
use strict;
use warnings;
use 5.010;
use List::Util qw[min max];
my $col1;
my $col2;
my $col3;
my $col4;
my $length;
my $gene;
my $exon;
my $est;
my $intron;
my $name = "Morten";
my $prev_length;
my $prev_gene;
my $prev_exon;
my $prev_est;
my $prev_intron;
my $prev_name = "Veno";
my $region;
my $chrS... |
0df5ffe17167bcfd44a4f7d5d7c0a01f35de7a456996f08a91328071a48bb471 | Perl | 2,659 | 86 | #!/usr/bin/perl
use Getopt::Std; %opt = ();
getopts("O:1:2:t:o:R:r:", \%opt);
$hg38na = "/home/groups/ravnica/refs/hg38/hs38d1_noalt_bsbolt/";
$mm10 = "/home/groups/ravnica/refs/mm10/bsbolt/";
$hybrid = "/home/groups/ravnica/refs/hybrid.hg19.mm10_bsbolt/";
$threads = 1;
$o_threads = 1;
$die = "
sciMET_align_BSBolt... |
c0f1b90471c2bd183b8e4ed7cbf6384aa8082811009455ed1865541d6fe82d5c | Perl | 2,769 | 88 | #!/usr/bin/perl
use Getopt::Std; %opt = ();
getopts("O:1:2:t:R:sr:u", \%opt);
$hg38na = "/home/groups/oroaklab/refs/hg38/hs38d1_noalt_bismark/";
$mm10 = "/home/groups/oroaklab/refs/mm10/bismark/";
$hybrid = "/home/groups/oroaklab/refs/bismark_hybrid.hg19.mm10/";
$threads = 1;
$die = "
sciMET_align_pe.pl (options)... |
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