sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
ebd65c1f98f37622a238441a7942c9a61b5b327d17ba68993e369d9043fdb38b | Python | 198,921 | 5,057 | # Copyright (C) 2022 Intel Corporation
# Copyright (C) CVAT.ai Corporation
#
# SPDX-License-Identifier: MIT
import io
import itertools
import json
import operator
import os
import os.path as osp
import re
import zipfile
from collections.abc import Generator, Iterable, Sequence
from copy import deepcopy
from datetime i... |
17629c28e92c711cac292ae6e6b373ac196a4f23df675841ef20865c50ba31b0 | Python | 200,000 | 2,919 | import os
import pandas as pd
import json
import nibabel as nib
import numpy as np
import glob
from cvdproc.config.paths import get_package_path
from nipype import Node, Workflow, MapNode, Function
from nipype.interfaces.utility import IdentityInterface, Merge, Select
from cvdproc.bids_data.rename_bids_file import rena... |
1bdfd27b95ae71f20c161e72c0615d7b7231b573edd177aa6f7b5475ecdb1ec5 | Python | 200,000 | 5,600 | # imagecodecs/tests/test_imagecodecs.py
# Copyright (c) 2018-2026, Christoph Gohlke
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# 1. Redistributions of source code must retain the above cop... |
31194dcaea05e6fbb4eff0aca4d73c773d86d0a02ab60e3cfa1d05056ea219c4 | Python | 200,000 | 5,243 | # coding: utf-8
"""Wrapper for C API of LightGBM."""
# This import causes lib_lightgbm.{dll,dylib,so} to be loaded.
# It's intentionally done here, as early as possible, to avoid issues like
# "libgomp.so.1: cannot allocate memory in static TLS block" on aarch64 Linux.
#
# For details, see the "cannot allocate memory ... |
3234a0688d0c638f6f5b33b13538251102058aeeb4f368d842614dd197097db8 | Python | 200,000 | 5,313 | """
An implementation of RESMAX:
"""
import torch
import torch.nn as nn
import torch.nn.functional as F
import torchvision.transforms as transforms
import torchvision
import numpy as np
import scipy as sp
import os
import time
import pdb
import random
from ._builder import build_model_with_cfg
from ._manipulate imp... |
36432a0622883d06006a566f26d853d6310105b1c56dcfdfacb0536173ef7d5f | Python | 200,000 | 3,285 | import datetime
import os
import shutil
import json
import sys
import numpy as np
from scipy.ndimage.morphology import binary_dilation
from dipy.align.transforms import RigidTransform3D
import subprocess
from elikopy.utils import makedir, update_status
import functools
print = functools.partial(print, flush=True)
de... |
42f3e77b132119549675559c5b92a05fbce38457f7ddeadec25bf66ed215a37d | Python | 200,000 | 4,303 | P={('B', 'a'): {('E', 'a'): -0.0050648453069648755,
('M', 'a'): -5.287963037107507},
('B', 'ad'): {('E', 'ad'): -0.0007479013978476627,
('M', 'ad'): -7.198613337130562},
('B', 'ag'): {},
('B', 'an'): {('E', 'an'): 0.0},
('B', 'b'): {('E', 'b'): -0.06753917715798491,
('M', ... |
59efcbc08b882808b0709620344da3769f59493597fbf1d0909d8c123c9b6e36 | Python | 200,000 | 4,564 | import pandas as pd
import numpy as np
import pickle
import seaborn as sns
from matplotlib import pyplot as plt
import matplotlib as mpl
import os
import copy
import pingouin as pg
import statsmodels.api as sm
from sklearn import metrics
from matplotlib.legend_handler import HandlerTuple
import statsmodels.formula.api ... |
7919e0e5df9ee14e6cf665a3aa79446e066d30dc4e60b2a7dd7abc3eb2b0b785 | Python | 200,000 | 6,425 | # imagecodecs/zarr.py
# Copyright (c) 2026, Christoph Gohlke
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# 1. Redistributions of source code must retain the above copyright notice,
# thi... |
8d70e9597646173559586fb8182433dea4a96c9e4a7d2a7d1463e354ec2ce8d7 | Python | 200,000 | 3,220 | from nested.utils import param_array_to_dict
import math
def update_EIANN_config_1_hidden_backprop_relu_SGD(x, context):
param_dict = param_array_to_dict(x, context.param_names)
learning_rate = param_dict['learning_rate']
context.training_kwargs['optimizer'] = 'SGD'
context.training_kwargs['learning... |
92b5c478e21d7f66a7471876581bd41a08d29f4577c45eb8f218efa03fecbda2 | Python | 200,000 | 4,553 | import os
from unittest import mock, TestCase
from unittest.mock import ANY, call
import kb_python.count as count
from kb_python.constants import (
ABUNDANCE_FILENAME,
ABUNDANCE_GENE_FILENAME,
ABUNDANCE_GENE_TPM_FILENAME,
ABUNDANCE_TPM_FILENAME,
ADATA_PREFIX,
BUS_CDNA_PREFIX,
BUS_FILENAME,
... |
a01e9c185b21fe1aa064238ed025fc8dc1974fad3bf2cef9dce1953e2688fb54 | Python | 200,000 | 3,129 | # -*- coding: utf-8 -*-
# Resource object code
#
# Created by: The Resource Compiler for PyQt5 (Qt v5.15.2)
#
# WARNING! All changes made in this file will be lost!
from PyQt5 import QtCore
qt_resource_data = b"\
\x00\x00\x06\x28\
\x00\
\x00\x15\xb6\x78\x9c\xed\x58\x4b\x6f\x1b\x55\x14\x3e\x1e\xcf\xd8\
\x5e\x40\x95\x... |
a6013843829505c56a1c992c1f2f290b84b367c936dadd7587988b16259b33cc | Python | 200,000 | 3,526 | #!/usr/bin/env python
# EDITABLE SECTIONS ARE MARKED WITH #@#
version="2.4"
authors=["Djurre de Jong", "Jaakko J. Uusitalo", "Tsjerk A. Wassenaar"]
# Parameters are defined for the following (protein) forcefields:
forcefields = ['martini21','martini21p','martini22','martini22p','elnedyn','elnedyn22','elnedyn22p',... |
b7309ce7e6b298834339f474ff03d9ed71b4ebba275b3676cfe9cdca0b8a8005 | Python | 200,000 | 7,097 | #!/usr/bin/env python
# -*- coding : utf-8 -*-
"""Various definitions of spherical sampling"""
import numpy as np
def dsigrid(odf_key="odf8") -> np.ndarray[float]:
"""Reads DSIStudio's ODF geometry in odfs.mat to use in creation of DSIStudio's
.fib file.
Parameters
----------
odf_keys : str; opt... |
c48ecff6f05382f255392da15a9f83c007c00aacc0161ad99d7b20c16b306d3f | Python | 200,000 | 4,533 | from __future__ import unicode_literals
P={('B', 'a'): {'\u4e00': -3.618715666782108,
'\u4e07': -10.500566885381515,
'\u4e0a': -8.541143017159477,
'\u4e0b': -8.445222895280738,
'\u4e0d': -2.7990867583580403,
'\u4e11': -7.837979058356061,
... |
c5cba445ac575677dde8d6c2e543687d22a7813b4f1f49aa17fe17ab10482b7b | Python | 200,000 | 5,339 | from __future__ import unicode_literals
P={'B': {'\u4e00': -3.6544978750449433,
'\u4e01': -8.125041941842026,
'\u4e03': -7.817392401429855,
'\u4e07': -6.3096425804013165,
'\u4e08': -8.866689067453933,
'\u4e09': -5.932085850549891,
'\u4e0a': -5.739552583325728,
'\u4e0b':... |
e08d7c45286a135c83d6bc6dc05aea862c9f19fc868bcb66b0cbb61bf8ea4540 | Python | 200,000 | 5,350 | """
An implementation of RESMAX:
"""
import torch
import torch.nn as nn
import torch.nn.functional as F
import torchvision.transforms as transforms
import torchvision
import numpy as np
import scipy as sp
import os
import time
import pdb
import random
from ._builder import build_model_with_cfg
from ._manipulate imp... |
e09358d3961a4c0f521081417e0bf9a1e59dad445d249b50019d6089b9a35704 | Python | 200,000 | 4,690 | # Generated by the protocol buffer compiler. DO NOT EDIT!
from google.protobuf import descriptor
from google.protobuf import message
from google.protobuf import reflection
from google.protobuf import descriptor_pb2
# @@protoc_insertion_point(imports)
DESCRIPTOR = descriptor.FileDescriptor(
name='caffe_b590f1d.pr... |
ee5cb9ebbb078224a5a3bcf381f2fe71ba8e3b3890c4150df92ab7226cb4d51e | Python | 200,000 | 7,725 | from __future__ import unicode_literals
P={'\u4e00': (('B', 'm'),
('S', 'm'),
('B', 'd'),
('B', 'a'),
('M', 'm'),
('B', 'n'),
('B', 'u'),
('E', 'r'),
('E', 'm'),
('M', 'd'),
('B', 's'),
... |
ef0dd3529eadd71f3b2eeb7ed3636d42d03415ecdf7b41d93765c7207882c43f | Python | 200,000 | 5,324 | #!/usr/bin/env python
#
# Copyright (c) 2009 Google Inc. All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyright
# notice, this list... |
f3d06786d8e94b4fc2b34f5410b9355d4608af52a8d24a51d6d800c558d41644 | Python | 200,000 | 5,349 | # Copyright (C) 2020-2022 Intel Corporation
# Copyright (C) CVAT.ai Corporation
#
# SPDX-License-Identifier: MIT
import copy
import io
import json
import logging
import os
import random
import shutil
import tempfile
import xml.etree.ElementTree as ET
import zipfile
from collections import defaultdict
from collections... |
f9fc611a09fd208d025bd11c26a516669a33373cf893ab410d4cf601765b1f09 | Python | 200,000 | 4,610 | # Generated by the protocol buffer compiler. DO NOT EDIT!
from google.protobuf import descriptor
from google.protobuf import message
from google.protobuf import reflection
from google.protobuf import descriptor_pb2
# @@protoc_insertion_point(imports)
DESCRIPTOR = descriptor.FileDescriptor(
name='caffe_6e3916.pro... |
57894457b46a4fc935d366191bea139a4d5478dfa67f731992a64a4aac720af6 | Python | 200,002 | 5,650 | # test_tifffile.py
# Copyright (c) 2008-2026, Christoph Gohlke
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# 1. Redistributions of source code must retain the above copyright notice,
# t... |
599912e91a8d0f2ef036816ef96f562d56cf30aae666dee269bbd41cf979a20e | Python | 200,003 | 3,849 | # Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
"""
Generate predictions using the Segment Anything Model (SAM).
SAM is an advanced image segmentation model offering features like promptable segmentation and zero-shot performance.
This module contains the implementation of the prediction logic and ... |
1b7917d20d62c7296c14a4b7f778f8fae7b36f93b667c95c33a19b13d46cb7a4 | Python | 200,004 | 4,686 | import os
import re
import logging
from abc import abstractmethod
from collections import Counter
from pathlib import Path
from typing import List, Union, Dict
import gensim
import numpy as np
import torch
from bpemb import BPEmb
from deprecated import deprecated
from torch.nn import ParameterList, Parameter
import ti... |
44fb0434534a2905b7e1870a5583e8f94f2a5d9b097eeb89b9058c10450d3654 | Python | 200,004 | 4,722 | import os
import re
import logging
from abc import abstractmethod
from collections import Counter
from pathlib import Path
from typing import List, Union, Dict
import gensim
import numpy as np
import torch
from bpemb import BPEmb
from deprecated import deprecated
from torch.nn import ParameterList, Parameter
import ti... |
6d2115469e2b3dde9697a66a4660a9e0530011b5d44a721065eff552afd9b5ec | Python | 200,004 | 4,505 | # The GUI will only work if the optional dependencies are installed, otherwise exit here
try:
import sys
import qdarkstyle
from PyQt6.QtCore import Qt, QPoint, QThread, pyqtSignal, QObject, QRegularExpression, QLocale
from PyQt6.QtGui import QEnterEvent, QFontMetrics, QSyntaxHighlighter, QTextCharFormat... |
259d4c276aba44a48164b3487db5c083feaaa462a321ce98fbae0f142bbca602 | Python | 200,005 | 5,139 | # tifffile.py
# Copyright (c) 2008-2026, Christoph Gohlke
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# 1. Redistributions of source code must retain the above copyright notice,
# this l... |
77157e86ea8e02dc07fc2bcd530f82b1122f17507d4ec88e5261b555a0fde15b | Python | 200,008 | 4,967 | # coding: utf-8
import copy
import itertools
import json
import math
import pickle
import random
import re
from pathlib import Path
from shutil import copyfile
import numpy as np
import psutil
import pytest
from scipy.sparse import csr_matrix, isspmatrix_csc, isspmatrix_csr
from sklearn.datasets import load_svmlight_f... |
6588afb842c18565060748e863517c065102f7d9ead67f58267b54e0282cfee0 | Python | 200,012 | 4,892 | """
Copyright 1999 Illinois Institute of Technology
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
"Software"), to deal in the Software without restriction, including
without limitation the rights to use, copy, modify, merge, publis... |
27e33a4ea50c1e7e97d6fad3a6ac2c252317683d4860b14a32f0531e58b58d7e | Python | 200,018 | 5,068 | """
Copyright 1999 Illinois Institute of Technology
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
"Software"), to deal in the Software without restriction, including
without limitation the rights to use, copy, modify, merge, publis... |
67a53d32d7578abfb87f0e60a3a7045a96e5edde85ac752f86279b2d51e79577 | Python | 202,969 | 4,191 | """Look at the spikes and bursts before trusting them.
Spike detection is the one step whose output the rest of the pipeline cannot
sanity-check for you: every firing rate, every correlation and every network
metric downstream is computed from whatever came out of it, and a threshold set
one MAD too low turns noise in... |
621eb403ff40c1ca4f13b49669ba7746e5cde168c0a53072b96812cc3f0ed3e1 | Quarto | 1,509 | 73 | ---
title: "Raw model / Robust"
subtitle: "Model ~group"
format:
html:
code-summary: "Show the code"
code-copy: true
toc: true
toc-depth: 3
execute:
warning: false
error: false
params:
model: "~group"
intercept: "WT"
method: "robust"
genome: mm10
txdb: TxDb.Mmusculus.UCSC.mm10.known... |
b0f1bb80f9d941cc674df68ca64b3b639d4f4e0faa01607aead51be823040746 | Quarto | 1,552 | 73 | ---
title: "Adjusted Model"
subtitle: "Model ~group + age + gender + sentrix_id"
format:
html:
code-summary: "Show the code"
code-copy: true
toc: true
toc-depth: 3
execute:
warning: false
error: false
params:
model: "~group+age+gender+sentrix_id"
intercept: "WT"
method: "ls"
genome: mm... |
7b6486a315f3936dd5fd9b2d50231b3d042261a428e4cd350935556499b0be6b | Quarto | 1,563 | 71 | ---
title: "Raw model"
subtitle: "Model ~group"
format:
html:
code-summary: "Show the code"
code-copy: true
toc: true
toc-depth: 3
execute:
warning: false
error: false
params:
model: "~group"
intercept: "WT"
method: "ls"
genome: mm10
txdb: TxDb.Mmusculus.UCSC.mm10.knownGene
dmrto... |
d5c30aba864857b5f8066088c0c92786d6075cdf38b344cc08a7a4cd2224d410 | Quarto | 1,565 | 73 | ---
title: "Adjusted Model / Robust"
subtitle: "Model ~group + age + gender + sentrix_id"
format:
html:
code-summary: "Show the code"
code-copy: true
toc: true
toc-depth: 3
execute:
warning: false
error: false
params:
model: "~group+age+gender+sentrix_id"
intercept: "WT"
method: "robust"
... |
744a9910a5390c8cdbe91685a307c94bd27dda312a9b67d885e6aab19b1e496e | Quarto | 1,640 | 75 | ---
title: "Raw model / Old only"
subtitle: "Model ~group"
format:
html:
code-summary: "Show the code"
code-copy: true
toc: true
toc-depth: 3
execute:
warning: false
error: false
params:
model: "~group"
intercept: "WT"
method: "ls"
genome: mm10
txdb: TxDb.Mmusculus.UCSC.mm10.knownGe... |
fc773bb8f3f9ab257dea509f53a129fe811bd4ef2161322470addb0b09b94e87 | Quarto | 1,653 | 75 | ---
title: "Raw model / Old only / Robust"
subtitle: "Model ~group"
format:
html:
code-summary: "Show the code"
code-copy: true
toc: true
toc-depth: 3
execute:
warning: false
error: false
params:
model: "~group"
intercept: "WT"
method: "robust"
genome: mm10
txdb: TxDb.Mmusculus.UCSC... |
1ddb7e5fa057aff4a56072dcd680805ac6d6034b5f14b7bb2e5f4e44157039a0 | Quarto | 1,690 | 75 | ---
title: "Adjusted Model / Young Only"
subtitle: "Model ~group + gender + sentrix_id"
format:
html:
code-summary: "Show the code"
code-copy: true
toc: true
toc-depth: 3
execute:
warning: false
error: false
params:
model: "~group+gender+sentrix_id"
intercept: "WT"
method: "ls"
genome:... |
087ef8494b061e7ecefa05f333e5e3b66244edb63e9e23eec67b6cf2107ab886 | Quarto | 1,703 | 75 | ---
title: "Adjusted Model / Young Only / Robust"
subtitle: "Model ~group + gender + sentrix_id"
format:
html:
code-summary: "Show the code"
code-copy: true
toc: true
toc-depth: 3
execute:
warning: false
error: false
params:
model: "~group+gender+sentrix_id"
intercept: "WT"
method: "robus... |
3d4fa6ee318464189ba03a5be11ffe34856906e6169beb341315839e970dc7fb | Quarto | 2,296 | 85 | ---
title: "Data Loading"
subtitle: "Loading methylation data and creating analysis objects"
params:
idat_path: "/data/EPI-AGING/files/ILL_20240614_epiaging_mm/idats/"
sample_sheet_path: "../sampleSheet.csv"
debug: true
---
This chapter covers the initial steps of loading methylation data from IDAT files and cre... |
f3be31aa23730cb1e54edc66d261dd4026d2d37e0d3f85e3d862bfbc750d5847 | Quarto | 2,701 | 87 | ---
title: "Methylation Analysis Workflow"
subtitle: "A comprehensive guide using methylkey"
author: "methylkey package"
date: today
---
# Welcome to methylkey
This book provides a comprehensive workflow for DNA methylation analysis using the **methylkey** R package. The workflow is organized into sequential chapters... |
3ed846a16ab2d69239f3b54bd17af195e6a9b1a48680c8bea6478e1ab1bd0ab8 | Quarto | 3,471 | 90 | ---
title: "Group Control"
subtitle: ""
format:
html:
code-summary: "Display code and parameters"
code-copy: true
execute:
warning: false
error: false
params:
groups: !expr c("sentrix_id","group","age","gender")
---
```{r setup}
#| echo: False
devtools::load_all("/home/cahaisv/git/methylkey2/")
```
`... |
21e534c0d7d23a327ec6722f6b68b5e715b4c92c958a5b7657b8f4df6bc7c9d4 | Quarto | 3,474 | 90 | ---
title: "Group Control"
subtitle: ""
format:
html:
code-summary: "Display code and parameters"
code-copy: true
execute:
warning: false
error: false
params:
groups: !expr c("sentrix_id","group","age","gender")
---
```{r setup}
#| echo: False
devtools::load_all("/home/cahaisv/git/methylkey2/")
```
`... |
636286ddc68fbc09cfa6fa1de5f26189dbe8a9c569bb118c8c380eeb51dec5fe | Quarto | 3,553 | 90 | ---
title: "Group Control / YOUNG only"
subtitle: ""
format:
html:
code-summary: "Display code and parameters"
code-copy: true
execute:
warning: false
error: false
params:
groups: !expr c("sentrix_id","group","gender")
---
```{r setup}
#| echo: False
devtools::load_all("/home/cahaisv/git/methylkey2/")... |
f21886702c1baa6b5c6fdfa6182909d7398e34ed8c020e24202121a49f68f969 | Quarto | 3,583 | 100 | ---
title: "Bath Correction"
subtitle: ""
format:
html:
code-summary: "Voir le code et les paramètres"
code-copy: true
execute:
warning: false
error: false
params:
groups: !expr c("sentrix_id","group","age","gender")
---
## Prerequisites
Load your processed methylation data:
```{r setup}
devtools::l... |
ba5d1ab6ded5bf3b571982f881dc8396316ff6a92fbb7d37e6794c4ac18aaec5 | Quarto | 4,107 | 135 | ---
title: "Quality Control and Data Assessment"
subtitle: "Assessing data quality and identifying issues"
format:
html:
code-summary: "Code"
code-copy: true
execute:
warning: false
error: false
params:
groups: !expr c("sentrix_id","group","age","gender")
---
```{r}
#| echo: False
devtools::load_all("... |
df78efc4846e722fc28ffa1d7b0c3f8f69d179358c64d40123d33f118fef2742 | Quarto | 6,934 | 219 | ```{r}
mrs <- get_results(mrs, index, tools=params$dmrtools, genome=params$genome, mvals=mvals, fdr = 0.2 )
model_file_name <- paste0(model_name, ".rds")
saveRDS(mrs, fs::path(output_dir, model_file_name))
```
### Differentially Methylated Probes
:::::::: panel-tabset
#### Summary
```{r}
#| code-summary: "Number of ... |
f3818e45d5c4d43f35eb15115f3ad0376cc6d9ea67b6580f50055eb8a815c1d5 | Quarto | 7,077 | 248 | ```{r}
mrs <- get_results(
mrs,
index,
tools = params$dmrtools,
genome = params$genome,
mvals = mvals,
fdr = 0.2
)
model_file_name <- paste0(model_name, ".rds")
saveRDS(mrs, fs::path(output_dir, model_file_name))
```
### Differentially Methylated Probes
:::::::: panel-tabset
#### Summary
```{r}
#| code-s... |
4dbcf1460ab1506a4cbc53471900c4fb5e79d721f0d3c332b67b7560515db7d4 | Quarto | 7,591 | 319 | ---
title: "Raport statystyczny"
format: docx
execute:
warning: false
message: false
docx:
reference-doc: references.docx
---
```{r, include=FALSE}
library(openxlsx)
library(tidyverse)
library(gt)
```
```{r, include = FALSE}
## wczetanie danych z Excela
dane <- read.xlsx("dane2.xlsx",sheet = 2)
```
#... |
dfd9f6704feb35aabcbf30a05666fdcc449b0e063efae0fb9c19a5a192259a7f | Quarto | 9,015 | 267 | ---
title: "syn_allograft_scRNAseq"
format: html
---
# 1. Setup
## 1.1 Imports
```{r imports}
wd = ""
setwd(wd)
library(tidyverse)
library(Seurat)
library(DESeq2)
library(ggrepel)
library(plotly)
```
## 1.3 Load Data
```{r Load Data}
syn_allo_so <- readRDS("path_to/seurat_obj.rds")
syn_allo_so <- UpdateSeuratObject... |
5cc327cbb37358a8de7a1ac748b8d5fe538a1be71dec9526b1f865bc700c8b52 | Quarto | 13,784 | 546 | ---
title: "Raport statystyczny"
format: docx
execute:
warning: false
message: false
docx:
reference-doc: references.docx
---
```{r, include=FALSE}
library(openxlsx)
library(dplyr)
library(tinytex)
library(ggpubr)
library(tidyverse)
library(gt)
library(pagedown)
library(ggplot2)
library(readxl)
library(fl... |
225eb8e92b0dfa707766f514923a1a280f4c230616ac32eb71eac67fe58c8cbc | Quarto | 16,744 | 648 | ---
title: "Raport statystyczny"
format: docx
execute:
warning: false
message: false
docx:
reference-doc: references.docx
---
```{r, include=FALSE}
library(openxlsx)
library(dplyr)
library(ggplot2)
library(readxl)
library(flextable)
library(knitr)
library(tidyr)
library(car)
library(glue)
library(purrr)
l... |
9015a0d82ae0e0ee80799927a558eca9f50edd3ecc8e88afffe35ab4565440ce | Quarto | 25,283 | 856 | ---
title: "Raport statystyczny"
format: docx
execute:
warning: false
message: false
docx:
reference-doc: references.docx
---
```{r, include=FALSE}
library(openxlsx)
library(dplyr)
library(tidyr)
library(flextable)
library(car)
library(glue)
```
```{r, include = FALSE}
dane <-... |
7f35708f3d8ef6189210cff7ece473fa74b3945e5eae731ba5c1986fd6f89fcf | Quarto | 28,950 | 316 | ---
title: "Response to reviewer comments"
format: html
editor: visual
---
## Reviews
Reviews for your submission to eLife: eLife-RP-RA-2025-108420
eLife Assessment\
This fundamental work significantly advances our understanding of gravity sensing and orientation behavior in the ctenophore, an animal of major impor... |
3154b876f16972b2dcb3b9cec7946a853c229e5ffdf39162f6541573387f1fe9 | Quarto | 52,074 | 1,453 | ---
title: "Brain communications- Demographics & models"
format: revealjs
editor: visual
---
## Load packages
```{r}
rm(list = ls())
pacman::p_load(tidyverse,
janitor,
rio,
here,
gt,
GGally,
gtExtras,
gtsummary,
... |
84991b1e16aa5f35deb1c365a1d2ea2198a6d78a3ea43f0429bbc1576ee2cd55 | Quarto | 54,497 | 955 | ---
title: Machine learning of factors for improving oyster hatchery production
author:
- Vyacheslav Lyubchich
- Matthew W. Gray
- Greg M. Silsbe
citation:
type: report
publisher: "University of Maryland Center for Environmental Science"
publisher-place: "Cambridge, Maryland, USA"
url: https://vlyubchic... |
a3b02a5acc01b72ac0f26436dac2b271bf9ef8edf3a2ad25c6cb7d0cd5f125a3 | Quarto | 57,542 | 1,234 | ---
title: "Spatial_Tumor_Analysis"
format: html
editor: visual
---
# 0 Setup
## 0.0 workding dir
```{r setup, include=FALSE}
wd <- ""
setwd(wd)
knitr::opts_knit$set(root.dir = wd)
```
## 0.1 Load Libraries
```{r Load Libraries}
# Seruat
library(Seurat)
library(hdf5r)
library(loupeR)
#general
library(tidyverse)
li... |
2fcffeb15b334f61f429c179d4dbaf176a2b2280c35a543aaa7c5b7b15be1982 | Quarto | 67,183 | 342 | ---
title: "Neural Connectome of the Ctenophore Statocyst"
subtitle: |
**Kei Jokura**$^{1,2,3,4,5*}$, **Sanja Jasek**$^{1,2,6}$, **Lara Niederhaus**$^{6}$, **Pawel Burkhardt**$^{7}$, **Gáspár Jékely**$^{1,2,6,*}$
<br><br>
$^{1}$ Living Systems Institute, University of Exeter, Exeter, EX4 4QD, United Kingdom ... |
a5102c2b41c5f6e19f85e29f9cb43c39b2310b6400f8e11a9b029e66f7a9d9fe | Quarto | 77,955 | 1,567 | ---
title: "Untitled"
format: html
editor: visual
---
## Load packages
```{r}
rm(list = ls())
pacman::p_load(tidyverse,
janitor,
rio,
here,
gt,
GGally,
gtExtras,
gtsummary,
tidymodels,
... |
c2ed78551673faeb92817c891891ec88d4b5326795cee372a852ff4aa8713110 | R | 30 | 1 | testthat::test_check("iTReX")
|
2285d2114f122bd64f498c84b18c20924011df9fc2fac22cc349cd3b25fd6d36 | R | 54 | 4 | library(testthat)
library(MOFA2)
test_check("MOFA2")
|
e8a2be4989320eba174397211eb65b83e399193c2cb8adf08a1d4d9f4d95d75a | R | 54 | 4 | library(testthat)
library(richR)
test_check("richR")
|
f38cdff87c6f8d6e97b399b720eb0ac9501f3a2d9831846420d468ff303bbfe9 | R | 61 | 3 | library(testthat)
library(wizbionet)
test_check("wizbionet")
|
2b7395d7f430b640bb37f4c66bf120ecf6fbe49d3e251c31a373aebb2faab02c | R | 63 | 5 | library(testthat)
library(pROC)
data(aSAH)
test_check("pROC")
|
d170f4baaf20fdaaae2af01e242c07543dc4f729a8bfb61d6aaf634e229eeec8 | R | 63 | 3 | "randomForest" <-
function(x, ...)
UseMethod("randomForest")
|
909ed980d63664f0e82d4e8cc3ef8b5f651b2b23560f23f78579484d44760a87 | R | 68 | 4 | library(testthat)
library(SVbyEye)
test_check(package = "SVbyEye")
|
b3dfd9fd72ac4335c100fc6a454c65925a9c4699771d5f5e1b1fcec23d2f5d77 | R | 78 | 3 |
set.seed(2023)
rings <- simulateDataset(n_cells=300, n_rings=4, n_genes=50)
|
9157041af35e8aaf76dfaa9906f24e3b7d3bb264df02fb56c05d41e68a8ac993 | R | 80 | 4 | test_that("iTReX works", {
skip_on_cran()
shinytest::expect_pass(test())
})
|
9be139e1b1edfe407261a21d0a0fa06a68a0154f2dc5f51b8dfe56dae7f0fb18 | R | 83 | 1 | install.packages(c('tidyverse','lme4','lmerTest','broom.mixed','ggplot2','readr'))
|
328490c8c7838a8682d122c2fdc05b90f07c38a47f976197a8b957da66e1b259 | R | 86 | 6 | library(shiny)
source("ui.R")
source("server.R")
shinyApp(ui = ui, server = server)
|
a7941ba76f1c1fea0b7fbb01675f725b91895ebc7f440fa8cbbfcc7e41dd6045 | R | 86 | 6 | source("../shinytest_helpers.R")
set_window()
get_tab_snapshots("iTReX")
shutdown()
|
db401e91ac838a53b216acd5c00d6b88d5164897b56982690729e1b599c936f2 | R | 89 | 5 | ##
## Set up common variables across scripts
##
PNG.OPT <- list(width=1600,height=1200)
|
3d5c6ff0c734e8fa99f9fa9f9fcc7fda092e0fd924f8ef3a1a83eff4c18c28a5 | R | 92 | 6 | library("UMI4Cats")
wk_dir = snakemake@params[['wk_dir']]
statsUMI4C(
wk_dir = wk_dir
) |
6c97fa1ca3f7c82ce53db8ca57011240820ab2b01738db7170ce4e30883cd7db | R | 93 | 1 | utils::globalVariables(c("ID","fID","UI","X","Y","nlvl","default","sampleID","dimred","grp")) |
9d31774deaeb400925d790fa4845a2240c0ebc350d51f549e99cf1716b06fa27 | R | 99 | 6 | source("../shinytest_helpers.R")
set_window()
app$snapshot(filename = "00_Home.json")
shutdown()
|
096187c604728887cd370d752c7c90c87c4ee82a38a093c8573fc2c9d576992f | R | 107 | 8 | ---
title: "cohort_heatmap"
output: html_document
---
```{r, fig.dim=c(width, height)}
cohort_heatmap
```
|
1f7c21d2a1731934911954d6c5c816e81d362e135bfad1cb6d14434151cfbe68 | R | 108 | 6 | source("../shinytest_helpers.R")
set_window(scale = 2)
app$snapshot(filename = "00_Home.json")
shutdown()
|
5739c529b474de1918608257029889b8ef082173736b4b22f66075a902a67657 | R | 108 | 3 | ################################# ED.Fig.1j
library(Nebulosa)
plot_density(reduced_all, features = "Kcng1")
|
86b4f3c44e50f7e625fca2e012815fc9beaa1967614595aa232d6fc027db51db | R | 108 | 11 | ##
## Libraries (needed by functions in this file)
##
##
library("gamlss")
##
## Analysis Functions
##
##
|
8ef903129379069f30f9d94dcab395e12ab2286e190ff26256b779e2e1859c7b | R | 108 | 6 | source("../shinytest_helpers.R")
set_window(scale = 1)
app$snapshot(filename = "00_Home.json")
shutdown()
|
4919d265b922d80c2865e3f969a0abcdd537853bf8e5454f289530194dbbce8d | R | 110 | 5 | message("pid = ", Sys.getpid())
options(shiny.autoreload = TRUE)
options(shiny.trace = TRUE)
shiny::runApp()
|
7afc746bb120b60135ddf894f7732dc4bb37c03e79bd3d815bdd7fb814a0a0e3 | R | 111 | 6 | library(testthat)
library(MOFA2)
test_check("MOFA2")
# setwd("/Users/rargelaguet/mofa/MOFA2/tests/testthat")
|
e1cc8a3c23cc0c3a1ead0a5f1c45077ef6d573ff1ee6e4a85fd7a0139b8ac7f7 | R | 111 | 6 | source("../shinytest_helpers.R")
set_window(scale = NULL)
app$snapshot(filename = "00_Home.json")
shutdown()
|
f650e1d43815cca111695653b09742e6571370af46a8b3e51ef9765fe7b1c413 | R | 115 | 5 | # This file is part of the standard test suite setup
library(testthat)
library(methylkey)
test_check("methylkey")
|
40df7109d72dcd23c6051980b835a01d6d4f567586c9b840ed8ecf5e78e64776 | R | 116 | 6 | source("../shinytest_helpers.R")
set_window()
run_hitnet_omics("BT-40_ST04", "BT-40_ST11", TRUE, 4, 4)
shutdown()
|
dd3c040920c92805ac2a7f019228bfc77a07445c1405fbdebd709adbd4d0bb0e | R | 119 | 6 | source("../shinytest_helpers.R")
set_window()
run_hitnet_omics("BT-40_ST04", "BT-40_ST11", FALSE, 10, 10)
shutdown()
|
f8c4ee3279e6069477512e073306dfd1f5042b382ffd171ce3a8984ae9f34696 | R | 119 | 6 | source("../shinytest_helpers.R")
set_window()
run_hitnet_omics("BT-40_ST04", "BT-40_ST11", TRUE, NULL, 4)
shutdown()
|
2a6aa147e0a84b0ebac1ce178a8c7d1cfe54974d4ea94450585160104a328d76 | R | 120 | 4 | rfNews <- function() {
newsfile <- file.path(system.file(package="randomForest"), "NEWS")
file.show(newsfile)
}
|
52c9b57c9ba196619493669654e2e5b29a9bb30230e1dc66b13695d55a0ca250 | R | 124 | 6 | source("../shinytest_helpers.R")
set_window()
run_hitnet_omics("INF-R-153_ST12", "INF-R-153_ST14", TRUE, 7, 7)
shutdown()
|
c00f558cddbc989b326850341083328aa6d7afd01b9ef963e58bd4c36c20d5bc | R | 126 | 3 | ################################# Fig.1j
#Read in the reduced_data R data from Fig.1i
VlnPlot(reduced_all, features = "Kcng1") |
91c544b238176eb2919c34afa13825ca7d9cdb45c2e015c110649f860f3c86de | R | 127 | 6 | source("../shinytest_helpers.R")
set_window()
run_hitnet_omics("INF-R-153_ST12", "INF-R-153_ST14", FALSE, 10, 10)
shutdown()
|
c4ed17a03c14342f109647be91635e7e5ed669f8caa5ba325e2bc2c9d26c98ce | R | 127 | 5 | library(fontawesome)
external_link <- function(href, text) {
a(href = href, target = "_blank", text, fa("external-link"))
}
|
f5d38c5179e456c3c6c8115207910036a07b1dfc606a971cbbec43249af688f7 | R | 131 | 6 | ############################
## iTReX Shiny tests file ##
## Author: Yannick Berker ##
############################
iTReX::test()
|
c19d51c61b0b7c0482817b53a83f9bb8c294c5a8ef4d9c5dc78ac0573be1206e | R | 135 | 9 | # To prevent lint errors when using .data and .env
utils::globalVariables(
c(
".env",
".data",
":=",
"density"
)
)
|
b1aac209c62860c2e43b076ad1a3944c7668cfbc39aaf4ade969082b8cf3426f | R | 139 | 1 | # null.roc <- structure(list(percent = FALSE, sensitivities = c(1, 0), specificities = c(0, 1), auc = NULL, class = "auc"), class = "roc")
|
2113ecff2c2186efeb91ae9d4d29808f6b4caf08fb9a7bdcf1536a5647b7a4ce | R | 145 | 3 | ################################# ED.Fig.1g
#Read in the reduced_data R data from Fig.1i
FeaturePlot(reduced_all, features = "Phox2b", label = T) |
a14564b4dd6297115f5544b4480776b8456b81a6dd16fda525e4502a19ae25be | R | 149 | 17 | ##
## Libraries (needed by functions in this file)
##
##
library("gamlss")
library("scales")
library("ggplot2")
##
## Plotting Functions
##
##
|
91234eb14b012749b49bcaac53d674ba70eba059a36ca3ad5dc2dd27768438b0 | R | 159 | 9 | ################################# ED.Fig.1i
DimPlot(
reduced_all,
group.by = "group",
split.by = "group",
reduction = "umap",
ncol = 2,
label = T
) |
d56b2da4c7cbb4c7ae4015d6f4508aa8efa67c99a86b61bdc5ab54f1952aaf30 | R | 159 | 7 | context("Loading the model")
library(MOFA2)
test_that("a pre-trained model can be loaded from disk", {
expect_is(load_model("test_mofa2.hdf5"), "MOFA")
})
|
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