sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
181b6bd53f5674be7cc19face499c71119600bb6a4ced5738d75e9d8511c3177 | Text | 19,059 | 186 | [](https://travis-ci.org/dpryan79/MethylDackel)
[](https://toolshed.g2.bx.psu.edu/)
[](https://snakemake.github.io)
[](https://... |
e9fc4c166d00458f2d0bbc9882137ed28e76240ce48b6d7bc26b4e7b643009aa | Text | 20,417 | 269 | # MotrpacRatTraining6moData
<!-- badges: start -->
[](https://zenodo.org/badge/latestdoi/511279465)
[
Bellybutton is a machine-learning-based image segmentation package, designed for ease of use. It uses a convolutional neural network, trained on images and paired user-generated masks, to classify pixels as "innies" or "outies" (inside or outside of a segmented region)... |
81375ac88de391b825d280805410b7acc79f7f18e75bea9da0398c7dc2fa2636 | Text | 21,003 | 352 | # pyCircos
Circos is one of the most popular software for visualizing genomic similarities and features. However, its execution process is complicated and requires multiple original config files for the visualizations. Additionally, Circos is written in Perl, which limits its integration with other software for biologi... |
676a84fc833e9f3e6f069445dd2eecb23cb599c99086032f17fd018e3857beaf | Text | 21,545 | 203 | # PyTorch-LBFGS: A PyTorch Implementation of L-BFGS
Authors: Hao-Jun Michael Shi (Northwestern University) and Dheevatsa Mudigere (Facebook)
## What is it?
PyTorch-LBFGS is a modular implementation of L-BFGS, a popular quasi-Newton method, for PyTorch that is compatible with many recent algorithmic advancements
for im... |
3fba18469d2059d04152c41c9ff355d72088f47df09a22793deed2fbc2bdfee2 | Text | 21,700 | 567 | MoTrPAC RNA-SEQ Pipeline
=================================================
[](https://zenodo.org/badge/latestdoi/144631622)
## Table of Contents
- [Overview](#overview)
- [Quick Start](#quick-start)
- [Prerequisites](#prerequisites)
- [GCP Set-up](#gcp-set-up)
- [Softwar... |
7f012049ecece8af1d02dc5b82c6fef6b3ed037b53fed20add9bf80effa915c3 | Text | 22,651 | 317 | # Bayesian Genome-wide (BGW) TWAS Software Usage
Tool **BGW-TWAS** is developed for leveraging both **cis-** and **trans-** eQTL based on a Bayesian variable selection model to predict genetically regulated gene expression (**GReX**). The product of estimated **cis-** and **trans-** eQTL effect sizes and their corresp... |
c67bd080e8ab571b55e706b3f49633ae64756e596e8d2779940635aeb5b083f4 | Text | 23,284 | 564 | # Repository for NEURON Model of Striatal Projection Neurons
This repository contains a NEURON + Python model of striatal projection neurons (or SPNs) designed to simulate the interaction between GABAergic and glutamatergic synaptic inputs.
It also provides all the R code used to produce the graph output (in particu... |
4aac35da65522a85af3e2424cb5166805f64016374aa24c5371821f25eeecb6b | Text | 24,156 | 326 | <img align="right" width="48" height="60" src="images/mapp_logo.png">
[](https://github.com/gruber-sciencelab/mapp/actions?query=workflow%3Aintegration)
[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.... |
cf1dca9833ba7133b0b179dfc088044ff25018aafb029a4fb9ed65e3a7150fb5 | Text | 24,156 | 326 | <img align="right" width="48" height="60" src="images/mapp_logo.png">
[](https://github.com/gruber-sciencelab/mapp/actions?query=workflow%3Aintegration)
[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.... |
5279b2641426045ae7169b05a238398a252718447c87f07efbbe688ec28120cd | Text | 25,932 | 405 | <p align="center"><img width="15%" src="examples/starspace.png" /></p>
# StarSpace
StarSpace is a general-purpose neural model for efficient learning of entity embeddings for solving a wide variety of problems:
- Learning word, sentence or document level embeddings.
- Information retrieval: ranking of sets of entiti... |
3f118b90ef66a392d0cba4827a7130757be0b2091321b2c0c4906ce15f1a64b0 | Text | 26,174 | 666 | 'ST_dataset.tgz' is a GZIP file containing the output of the Space Ranger for Visium spatial transcriptomics datasets.
The directory structure is as follows:
├── P301L.17mo.1
│ ├── filtered_feature_bc_matrix
│ │ ├── barcodes.tsv.gz
│ │ ├── features.tsv.gz
│ │ └── matrix.mtx.gz
│ ├── filtered_f... |
47f4a54bf578c2aed7acbcf9ee1c13124221c4e141345836e85f8028476bae48 | Text | 26,357 | 489 | # FID-Net
Deep Neural Networks for Analysing NMR time domain data. See:
* [G Karunanithy and D F Hansen (2021, JBNMR)](https://doi.org/10.1007/s10858-021-00366-w)
* [G Karunanithy, H W Mackenzie and D F Hansen (2021, JACS)](https://doi.org/10.1021/jacs.1c04010)
* [G Karunanithy, V K Shukla and D F Hansen (2023, bioRxi... |
fb77a9766e47118851ad3cd5606bf7acfff323a59b208043342a956cbe3fe0cc | Text | 27,464 | 671 | # SpeedSeq
A flexible framework for rapid genome analysis and interpretation
C Chiang, R M Layer, G G Faust, M R Lindberg, D B Rose, E P Garrison, G T Marth, A R Quinlan, and I M Hall. SpeedSeq: ultra-fast personal genome analysis and interpretation. Nat Meth (2015). doi:10.1038/nmeth.3505.
http://www.natu... |
3ded2456869e0a21fd96c1de1b47287aadab02ad37c53dbc98d633145352f3f1 | Text | 28,070 | 762 | MoTrPAC RRBS Pipeline
=================================================
[](https://zenodo.org/badge/latestdoi/161703075)
## Table of Contents
- [Overview](#overview)
- [Quick Start](#quick-start)
- [Prerequisites](#prerequisites)
- [GCP Set-up](#gcp-set-up)
- [Software /... |
494588039cc2de3fc02c74dcda13946e56b9dc1c82d5c0602cdaa9bc2809fc01 | Text | 28,493 | 456 | # STAMP tool kit
**`stamp`** is a set of computational tools developed for processing sequencing data from **mt-STAMP** (**s**equencing by **t**argeted **a**mplification of **m**ultiplex **p**robes) which is a labor- and cost-effective sequencing method designed for assessing human mitochondrial DNA (mtDNA) variations... |
8d5b95c4afa3210814d33b8aedde1517cc65fefe8c4c5440cd6ab05c5c6705be | Text | 30,454 | 403 | # MONAI Tutorials
This repository hosts the MONAI tutorials.
### 1. Requirements
Most of the examples and tutorials require
[matplotlib](https://matplotlib.org/) and [Jupyter Notebook](https://jupyter.org/).
These can be installed with:
```bash
python -m pip install -U pip
python -m pip install -U matplotlib
python ... |
6ac981004cffe8c74f320810e1f2928c3628fd4abff08478e6f0fc761ea7a5be | Text | 32,335 | 766 | ## R analysis for Day et al., 2023
Recreates graphical outputs and statistical analyses in the manuscript:
Day M., Belal M., Surmeier W. C., Melendez A., Wokosin, D., Tkatch T., Clarke V. R. J. and Surmeier D. J.
State-dependent GABAergic regulation of striatal spiny projection neuron excitability (2023) (Working ti... |
7ab8b2237e99b67e8c4d6b2d05acd1b2338336029e7901c4cf70e511650db6c1 | Text | 34,640 | 229 | # OpenFF Force Fields
[](https://github.com/openforcefield/openff-forcefields/actions?query=branch%3Amain+workflow%3ACI)
This repository contains force fields released by the [Open Force Field Initiative](https://openforcefie... |
9aef0544fdd829b532a4ad3aee2ee9e89fc1e31d4bb673125632b8b3007ee421 | Text | 37,932 | 311 | <p align="center">
<img src="resources/CraniumPy_logo.png" alt="CraniumPy logo" width="220">
</p>
# CraniumPy
* [Description](#description)
* [Download](#download)
* [Usage](#usage)
* [Getting started](#getting-started)
* [Preprocessing and landmarks](#preprocessing-and-landmarks)
* [Registration... |
d89eb9790ce805ce23e1b1a6804f4d67c81056025e4852b875f8ddfd87a08125 | Text | 48,907 | 584 | # RF*diffusion*
<!--
<img width="1115" alt="Screen Shot 2023-01-19 at 5 56 33 PM" src="https://user-images.githubusercontent.com/56419265/213588200-f8f44dba-276e-4dd2-b844-15acc441458d.png">
-->
<p align="center">
<img src="./img/diffusion_protein_gradient_2.jpg" alt="alt text" width="1100px" align="middle"/>
</p>
... |
dc2f9696e6b996451c8c811ed129357241e3a1b0bba56f7c7791c8015b7ca6c4 | Text | 60,848 | 846 | # MoTrPAC ATAC-Seq QC and Analysis Pipeline
[](https://zenodo.org/badge/latestdoi/221818534)
## Overview
This repository provides MoTrPAC-specific supplements to the [ENCODE ATAC-seq pipeline](https://github.com/ENCODE-DCC/atac-seq-pipeline).
### ATAC-Seq Method
**ATAC... |
506aee4ee46d19877d530e85629f584960dc3813c29567d2d8e75fc4724670c8 | Text | 63,743 | 322 | # Semi-supervised-learning-for-medical-image-segmentation.
* **[New] We have transferred to a new topic about active learning and source-free domain adaptation for medical image analysis, which may be closer to the real clinical requirement. The new benchmark is [here](https://github.com/whq-xxh/ADA4MIA).**
* We are re... |
7b9ce856345217f70fd77b2ba7b49f2f1f868a9e93ffb35d54466f5ace285602 | Text | 69,618 | 1,048 | # FramebyFrame R package
Francois Kroll, 2022 @Rihel lab, UCL.
FramebyFrame is an R package to analyse behavioural trackings of zebrafish larvae, mainly using the DanioVision (Noldus) or the Zebrabox (Viewpoint) in "Quantization" mode.
Already using the Zebrabox? Read below ([Frame-by-frame manifesto](#The-frame-b... |
fd0389638dc24c3569a559df7f9f149ce055dbf6456ee1a0cfd939509a7c2a17 | Text | 95,703 | 701 | [](https://zenodo.org/badge/latestdoi/363765458)
# BrainSurfer
<img align="left" width="250" height="300" src="https://i.imgur.com/Q0AJWcn.png">
BrainSurfer is a MATLAB toolbox for visualizing brain surfaces and showing statistical maps on top of them.
<br/>
<br/>
It se... |
69dee313d6982ef86199c0e8cb0f5ad9aca683bf2250418a872fcbbcc00d514b | Text | 107,230 | 1,022 | # 🐇 meshoptimizer [](https://github.com/zeux/meshoptimizer/actions) [](https://codecov.io/github/zeux/meshoptimizer?branch=master) [
# Conformal Prediction: The Definitive Resource [](https://awesome.re) [](https://zenodo.org/badge/latestdoi/436989758)
... |
38233bb0194b855bb4cd2ef155f18540458859414f234e54dc38e6dd834f5612 | TypeScript | 71 | 2 | import DownloadsPage from "./DownloadsPage";
export { DownloadsPage };
|
eef67ee02e504f4692ee50e4d2e1b4cc212e7c673b27afc3c7b04cc21299634a | TypeScript | 83 | 3 | import YAxis from "./yaxis";
import XAxis from "./xaxis";
export { YAxis, XAxis };
|
901f79b9fa61111ac39d3067c6d0fd5fcb4c00edd19157ec9c505930ab12f98d | TypeScript | 110 | 3 | import HomePage from "./HomePage";
import AboutUsPage from "./AboutUsPage";
export { HomePage, AboutUsPage };
|
d70e7245ad657cf7c6142995317e99c322ec5967891a6d7d3691c7ee6d8eec2c | TypeScript | 129 | 7 | export type AxisProps = {
width: number;
height: number;
range: [number, number];
title: string;
fontStyle: string;
};
|
737d6cd5523c8bf092c97400d818b4c732d96e868785b44183d9fd2f2d2c0f1d | TypeScript | 133 | 8 | export interface TrackTemplate {
title: string;
url: string;
}
export interface TrackList {
[key: string]: TrackTemplate[];
}
|
59e31487789a39b08397b9659a75782abcd3d9d00d26f77696d7f22df1bf130d | TypeScript | 148 | 8 | import StandaloneApp from './StandaloneApp.svelte';
const app = new StandaloneApp({
target: document.body,
props: {},
});
export default app;
|
e38fa31ce535d577a484aefc4e6261abf5ec35268a1462ec837ce40fc4348c44 | TypeScript | 151 | 5 | // Copyright (c) venkatesh-sivaraman
// Distributed under the terms of the Modified BSD License.
export * from './version';
export * from './widget';
|
ddcf0b3c8c304d9c69d67d863730a037314d161ba17fdb44ad54ed8268b83f04 | TypeScript | 173 | 3 | import EpigeneticTracksModal from "./EpigeneticTracks";
import ConservationTrackModal from "./ConservationTracks";
export { EpigeneticTracksModal, ConservationTrackModal };
|
917002075ea95a08edefc5102ff3bd1e920f17e623ea35e6f44150d95f5d81f0 | TypeScript | 198 | 5 | export * from './meshopt_encoder.js';
export * from './meshopt_decoder.js';
export * from './meshopt_simplifier.js';
export * from './meshopt_clusterizer.js';
export * from './meshopt_tangents.js';
|
15cb48f4423f75f709a3e5b7d8c7c6110caa428c6c2b72beac81ff5b4075748c | TypeScript | 235 | 4 | import EpigeneticTracks, { tracks } from "./EpigeneticTracks";
import VariantTracks from "./VariantTracks";
import ConservationTracks from "./ConservationTracks";
export { EpigeneticTracks, tracks, VariantTracks, ConservationTracks };
|
c261337d5c5512bf5d4d890646d4e10e5263de8d2c78cc48036eb968d1447cc0 | TypeScript | 241 | 5 | // jest-dom adds custom jest matchers for asserting on DOM nodes.
// allows you to do things like:
// expect(element).toHaveTextContent(/react/i)
// learn more: https://github.com/testing-library/jest-dom
import "@testing-library/jest-dom";
|
fe19de1560befe81ac4b571437fca7d44128caea2c08919a21fe375c646c014b | TypeScript | 267 | 6 | import { reducer, actions } from './actions'
import { sagas, saga_actions } from './sagas'
import * as selectors from './selectors'
import WorldlinesPanel from './components/WorldlinePanel'
export { reducer, actions, sagas, saga_actions, selectors, WorldlinesPanel } |
002031dee3b02b09491fe769fcde64b2d2e6dddfc10048bee374e52a27933e70 | TypeScript | 269 | 6 | import { reducer, actions } from './actions'
import { sagas, saga_actions } from './sagas'
import * as selectors from './selectors'
import ProvenancePanel from './components/ProvenancePanel'
export { reducer, actions, sagas, saga_actions, selectors, ProvenancePanel }
|
768649b4fcd35e1026cd317ab7075c0bdde3914070de8bcc2dde94a37bd6e247 | TypeScript | 293 | 11 | export type provenance_id_t = string
export type Provenance_t = {
id: provenance_id_t,
visible: boolean,
}
export type ProvenancesState_t = {[key: string]: Provenance_t}
// This is the model of our module state (e.g. return type of the reducer)
export type State_t = ProvenancesState_t
|
d1c122b5bcdbe9fae55cd2f26b755cea4f0968809ae379416d6b884ad0497409 | TypeScript | 311 | 5 | import DiseaseTraitPortal from "./DiseaseTraitPortal/DiseaseTraitPortal";
import SNPPortal from "./SnpPortal/SNPPortal";
import GenePortal from "./GenePortal/GenePortal";
import SingleCellPortal from "./SingleCellPortal/SingleCellPortal";
export { DiseaseTraitPortal, SNPPortal, GenePortal, SingleCellPortal };
|
33279e7347085de22e945450e4a9d528fd2bd265e53131ca5c6d454bb7a7a3b0 | TypeScript | 341 | 8 | import {reducer, actions} from './actions'
import { sagas, saga_actions } from './sagas'
import * as selectors from "./selectors"
import AnnotationsSVG from './components/AnnotationsSVG'
import AnnotationPanel from './components/AnnotationPanel'
export {AnnotationsSVG, AnnotationPanel, actions, saga_actions, reducer,
... |
80652d11906b5aa27c657c2db15cff6d6232ec664a310ca3bcdf4e7cd4032b54 | TypeScript | 345 | 13 | export const PORTAL_SELECT_OPTIONS = [
{
value: "disease/trait",
name: "Disease/Trait",
helperText: "e.g. schizophrenia, years of education",
},
{ value: "gene/bcre", name: "Gene/b-cCRE", helperText: "e.g., APOE, MBP, PCP4" },
{
value: "snp/qtl",
name: "SNP/QTL",
helperText: "e.g. rs2836... |
7f3254ef8828c1b9f181073b91eeb74d15b7fa1478d86afb324616e2a41fb7ac | TypeScript | 363 | 14 | import { createSelector } from 'reselect'
import * as app_selectors from '../app/selectors'
export const get_state = app_selectors.get_provenances_state
export const get_visible_provenances = createSelector(
get_state,
(x) => {
console.log(x)
return Object.entries(x)
.filter((p) => p[... |
8d4b9db076f4c0b684fc3ece18bfa96bdf27b71ee9bfd7dcbd44721031a98e2a | TypeScript | 377 | 15 | import { reducer, actions } from './actions'
import { sagas, saga_actions } from './sagas'
import * as selectors from './selectors'
import AnnotationWindowTest from './components/AnnotationWindowTest'
import AnnotationWindow from './components/AnnotationWindow'
export {
reducer,
actions,
sagas,
saga_actions,
... |
91c3db74e20996be81215988262af8675305413b79d4fd5e9a2895eb01f5a169 | TypeScript | 403 | 17 | import { createSelector } from 'reselect'
import * as app_selectors from '../app/selectors'
export const get_state = app_selectors.get_worldlines_state
export const get_worldlines = createSelector(
get_state,
(s) => s.worldlines
)
export const get_visible_worldlines = createSelector(
get_worldlines,
(s) => ... |
780f64898ef44a68c0e45687a54528aa19e2c56d9c83940dee7a74c4a3430bfd | TypeScript | 425 | 15 | import { ReportHandler } from "web-vitals";
const reportWebVitals = (onPerfEntry?: ReportHandler) => {
if (onPerfEntry && onPerfEntry instanceof Function) {
import("web-vitals").then(({ getCLS, getFID, getFCP, getLCP, getTTFB }) => {
getCLS(onPerfEntry);
getFID(onPerfEntry);
getFCP(onPerfEntry)... |
994f5ef6846c662a6e3fc36a177096d2dc385eebe1485c32b5d6dac61f14fc7b | TypeScript | 452 | 13 | export function ticks(range: [number, number], cscale: number = 1.0): number[] {
const sfig = Math.pow(10.0, Math.floor(Math.log10(range[1])));
const r: number[] = [],
lrange = [
Math.floor(range[0] / sfig) * sfig,
Math.ceil(range[1] / sfig) * sfig,
];
for (let i = lrange[0]; i <= lrange[1]; i... |
91e3b778826e33582e33194c648c6b995981f4b5516a9872f730b40922194e1c | TypeScript | 456 | 12 | import type { AnnotationWindowState_t } from '../annotation_window/model'
import type { AnnotationsState_t } from '../annotations/model'
import type { WorldlinesState_t } from '../worldlines/model'
import type { ProvenancesState_t } from '../provenances/model'
export type State_t = {
annotation_window: AnnotationWin... |
b0ec2dd6d754180181dec8207478efcf2b294080355182f21a953618259504d2 | TypeScript | 468 | 16 | import styled from "@emotion/styled";
import { Tab } from "@mui/material";
import ToggleButton from "@mui/material/ToggleButton";
import { Button } from "@weng-lab/psychscreen-ui-components";
export const StyledTab = styled(Tab)(() => ({
textTransform: "none" as any,
}));
export const StyledButton = styled(Button)(... |
84a0ba2fb3d08785a50a397a278b3d6cb8f39f1848ad09ab5c847c708ec179ca | TypeScript | 470 | 16 | import { State_t } from './model'
export const get_annotation_window_state = (app_state: State_t) =>
app_state.annotation_window
export const get_annotations_state = (app_state: State_t) =>
app_state.annotations
export const get_worldlines_state = (app_state: State_t) =>
app_state.worldlines
export cons... |
850ed4d19baaa880db28219845034ebc9664adf7d8fa5ddc2e7ab59a57b8f0a3 | TypeScript | 470 | 18 | import { worldline_id_t } from "../worldlines/model";
export type annotation_id_t = number;
export type Annotation_t = {
id: annotation_id_t,
x: number, // 0 : 1 float32
y: number, // 0 : 1 float32
z: number, // 0 : 1 float32
t_idx: number, // 0 : (shape_t-1) uint32
worldline_id: worldline_id_t // uint32
... |
2314d28891d180c18acc420ae1f0db1c29cdfadbe395092cf9505099b0fe0f28 | TypeScript | 503 | 18 | // Copyright (c) venkatesh-sivaraman
// Distributed under the terms of the Modified BSD License.
// eslint-disable-next-line @typescript-eslint/no-var-requires
const data = require('../package.json');
/**
* The _model_module_version/_view_module_version this package implements.
*
* The html widget manager assumes ... |
1bddf531d112a3981087c9022a06e6179aeaf6cc70374cc00b7212212ca69f19 | TypeScript | 580 | 23 | import { useState, useEffect } from "react";
function getWindowDimensions() {
const { innerWidth: width, innerHeight: height } = window;
return {
width,
height,
};
}
export function useViewportSize() {
const [windowDimensions, setWindowDimensions] = useState(
getWindowDimensions()
);
useEffect... |
5d23019d86e981bdbce3f697dc8e572bbdd5b17351bc42227fff2ed11a336c45 | TypeScript | 615 | 16 | // Copyright (c) Jupyter Development Team.
// Distributed under the terms of the Modified BSD License.
// Entry point for the notebook bundle containing custom model definitions.
//
// Setup notebook base URL
//
// Some static assets may be required by the custom widget javascript. The base
// url for the notebook is ... |
1ecf17d92a4bc93966c290fba2a2a3549a3b16f0e07de77ec7ecbfb77e4cfae1 | TypeScript | 648 | 25 | export type worldline_id_t = number
export type worldline_category_t = string
export type color_t = string
export type Worldline_t = {
id: worldline_id_t,
name: string,
// url: string | null,
// lineage: string | null,
// description: string | null,
color: color_t,
visible: boolean,
}
export type World... |
0b3a271825a6c23c98b3110ce5203c772b19080ff5d0b165d230b9b13372d246 | TypeScript | 710 | 25 | // import type { worldline_id_t } from '../worldlines/model'
// import { annotation_id_t } from '../annotations/model'
// export type AnnotationWindowState_t = {
// x: number,
// y: number,
// z: number,
// c_idx: number,
// t_idx: number,
// shape_x: number,
// shape_y: number,
// shape_z: number,
// ... |
3a28d62fba823911f2f70c31ae6c503e7e35d36ac2721ff796e9ff0ff824eb9e | TypeScript | 710 | 23 | import { TrackList } from "../types";
export const EvoConservationTracks: TrackList = {
"Conservation Tracks": [
{
title:
"240-mammal phyloP conservation score (Vertical Viewing Range [-2 to 9])",
url: "https://downloads.wenglab.org/241-mammalian-2020v2.bigWig",
},
{
title: "100... |
6c5596bcbb84ed52fec8af95809b3ab2ed5bc44c1f174ca967ce875702bf195d | TypeScript | 743 | 36 | import { createSlice, PayloadAction } from '@reduxjs/toolkit'
import {
AnnotationsState_t as State_t ,
Annotation_t,
annotation_id_t
} from './model'
export const initialState: State_t = {}
const reducers = {
set_state: (state: State_t, action: PayloadAction<State_t>) =>
action.payload,
set_annotatio... |
0fc8187d59f0a6a2978186849e9debe64c547ec5d7283b8d5a9686b8ef1c271c | TypeScript | 792 | 28 | // This file is part of meshoptimizer library and is distributed under the terms of MIT License.
// Copyright (C) 2016-2026, by Arseny Kapoulkine (arseny.kapoulkine@gmail.com)
export type TangentsFlags = 'Compatible' | 'ZeroFallback';
export const MeshoptTangents: {
supported: boolean;
ready: Promise<void>;
gener... |
6ada18026c66751c50b1a3c6b331e7d4180ae9a980c2c8b67836fb52e87d0dac | TypeScript | 800 | 37 | import { createSlice, PayloadAction } from '@reduxjs/toolkit'
import {
provenance_id_t,
ProvenancesState_t as State_t,
} from './model'
export const initialState: State_t = {}
const reducers = {
set_state: (_state: State_t, action: PayloadAction<State_t>) =>
action.payload,
set_provenance_selected: (
... |
2b1e0eadd69ac66e6cd365cf76822fdfb4a1ec7dcb330f65670d0dc2735d0881 | TypeScript | 813 | 32 | import type { Writable } from 'svelte/store';
import { writable } from 'svelte/store';
export function syncValue(model: any, name_: string, defaultVal: any) {
const name: string = name_;
const curVal: Writable<any> = writable(model.get(name) || defaultVal);
model.on('change:' + name, (model: any, val: any) => c... |
11bd59a8e188ce7eb79b3a94781e10a9156c2cd9c3d812dcf0fe1240b3107cf4 | TypeScript | 838 | 35 | import { combineReducers } from 'redux'
import {
actions as annotation_window_actions,
reducer as annotation_window_reducer
} from '../annotation_window'
import {
actions as annotations_actions,
reducer as annotations_reducer
} from '../annotations'
import {
actions as worldlines_actions,
reducer as worl... |
4d0b1a62a4b35c67dfed7f1675869cb7ebd4f662c6870eeb4494c7a6ab9e4029 | TypeScript | 863 | 37 | import { all } from 'redux-saga/effects'
import {
sagas as annotation_window_sagas,
saga_actions as annotation_window_saga_actions,
} from '../annotation_window'
import {
sagas as annotations_sagas,
saga_actions as annotations_saga_actions,
} from '../annotations'
import {
sagas as worldlines_sagas,
saga... |
804e95c2fea13467a2e8002a8aa41fb470a17b3fea5a8d7eaaa156c635c03a70 | TypeScript | 870 | 15 | // This file is part of meshoptimizer library and is distributed under the terms of MIT License.
// Copyright (C) 2016-2026, by Arseny Kapoulkine (arseny.kapoulkine@gmail.com)
export const MeshoptDecoder: {
supported: boolean;
ready: Promise<void>;
decodeVertexBuffer: (target: Uint8Array, count: number, size: numbe... |
3b093df557e6aa7d43ceb2487fd9b79dd39b8964460df7783b3b794f18ace1da | TypeScript | 918 | 41 | import type { worldline_id_t } from '../worldlines/model'
import { annotation_id_t } from '../annotations/model'
export type rpc_t = {
name: string,
default_args: string,
docstring: string,
}
export type LUT_t = {
red: [number, number],
green: [number, number],
blue: [number, number]
}
export type Annota... |
899be956a4a0c82059eef6a43f27f61cd330c3641901daad458017e60eb348fa | TypeScript | 927 | 28 | export const DEFAULT_TRACKS_HG38: Map<string, { url: string }> = new Map([
["rDHSs", { url: "gs://gcp.wenglab.org/GRCh38-rDHSs.bigBed" }],
["cCREs", { url: "gs://gcp.wenglab.org/GRCh38-cCREs.bigBed" }],
["DNase", { url: "gs://gcp.wenglab.org/dnase.GRCh38.sum.bigWig" }],
]);
export const DEFAULT_TRACKS_MM10: Map<... |
69b506921ecf405c555688307b4f78cefec444a09b98c1a647b9163b1133b8c3 | TypeScript | 971 | 34 | import { TrackList } from "../types";
export const PseudobulkAtacTracks: TrackList = {
"Pseudo bulk ATAC": [
{
title: "Microglia",
url: "https://downloads.wenglab.org/pseudobulkatac/Microglia.bigWig",
},
{
title: "Astrocytes",
url: "https://downloads.wenglab.org/pseudobulkatac/Ast... |
59a183b813c753f7957e998775421d02b1a2ce6767aec1800ca64c4e50089899 | TypeScript | 1,000 | 38 | import { TrackList } from "../types";
export const AtackSeqPeaksTracks: TrackList = {
"ATAC Seq Peaks": [
{
title: "Astrocytes",
url: "https://downloads.wenglab.org/Astro.PeakCalls.bb",
},
{
title: "Endothelial Cells",
url: "https://downloads.wenglab.org/Endo.PeakCalls.bb",
},... |
ee50dc159e7e79a82577240ed8555d42e469165ea42abd7dcdccb6d92879e063 | TypeScript | 1,113 | 38 | import { createAction, PayloadAction } from '@reduxjs/toolkit'
import { put, takeEvery, select } from 'redux-saga/effects'
import { actions } from './actions'
import { ProvenancesState_t } from './model'
import { Annotation_t } from '../annotations/model'
import * as annotations_selectors from '../annotations/selecto... |
0e882d5f1ee7d2dc3d0703ba2aa83cffc25df4594b35646e9dfe6a3600ca91d4 | TypeScript | 1,114 | 33 | import { Canvg } from "canvg";
import html2canvas from "html2canvas";
export function downloadSVGAsPNG(svgElement: SVGElement, filename: string) {
// Create a canvas element
const canvas = document.createElement("canvas");
const ctx = canvas.getContext("2d");
if (!ctx) return;
// Get the SVG element's dimen... |
a7cd25f9c23672a7db5e84191eb78b03235030dd74039e244240aa2f1329cbb9 | TypeScript | 1,132 | 42 | // Copyright (c) venkatesh-sivaraman
// Distributed under the terms of the Modified BSD License.
import type { Application, IPlugin } from '@phosphor/application';
import type { Widget } from '@phosphor/widgets';
import { IJupyterWidgetRegistry } from '@jupyter-widgets/base';
import * as widgetExports from './widge... |
c9f97c72c05d1eaf18b812040bf6e6b1203d2ca5425bd644b3eea0b4673ec6cd | TypeScript | 1,196 | 34 | // Convert x/y/z to index values using shape. The convention is that images
// go from 0.0 to 1.0, so the center values of each pixel are in (0, 1)
import { LUT_t } from "./model"
export const idx_from_coord = (coord: number, shape: number): number => {
return Math.max(Math.floor(coord * shape - 1e-6), 0)
}
export ... |
e891f3b923bca88991a816ee351f48a2d469bd0c69ee9e62d103abb3bc7833f1 | TypeScript | 1,243 | 42 | import { GenomeExplorerState, GenomicRange } from "./GenomeExplorer";
export enum GenomeExplorerActions {
GENOME_EXPLORER_DOMAIN_CHANGED = "GENOME_EXPLORER_DOMAIN_CHANGED",
GENOME_EXPLORER_REGION_HIGHLIGHTED = "GENOME_EXPLORER_REGION_HIGHLIGHTED",
}
export type GenomeExplorerDomainChangedAction = {
type: Genome... |
f868b697558e46765eba7dc57b8c720863cbf53020deb64f9c6da186a13b07dd | TypeScript | 1,267 | 49 | // Copyright (c) venkatesh-sivaraman
// Distributed under the terms of the Modified BSD License.
import {
DOMWidgetModel,
DOMWidgetView,
ISerializers,
} from '@jupyter-widgets/base';
import { MODULE_NAME, MODULE_VERSION } from './version';
import App from './App.svelte';
export class ViewerModel extends DOMWi... |
12a23a0e2e221b9451115a3ec45350911b98afe6aba9a2e8db40995252b162da | TypeScript | 1,285 | 56 | import { gql, useQuery } from "@apollo/client";
import { ManhattanPoint } from "genomebrowser-test";
import { ldTrack, manhattanTrack } from "./useManhattanData";
export const ldQuery = gql(`
query snips_in_ld($id: [String]) {
snp: snpQuery(assembly: "hg38", snpids: $id) {
linkageDisequilibrium(rSquaredThr... |
390ff27f49d670c19ec34624e4db54d37820a994b3b673ea6865c784d7139f09 | TypeScript | 1,441 | 64 | import { createSlice, PayloadAction } from '@reduxjs/toolkit'
import {
worldline_id_t,
Worldline_t,
Worldlines_t,
WorldlinesState_t as State_t,
} from './model'
export const initialState: State_t = {
worldlines: {},
worldline_lists: null,
selected_lists: []
}
const reducers = {
set_state: (state: St... |
4c769e430f99a67a55ed23c981ab6b51e1587a93479d328ba16ffc08289d39a9 | TypeScript | 1,448 | 23 | // This file is part of meshoptimizer library and is distributed under the terms of MIT License.
// Copyright (C) 2016-2026, by Arseny Kapoulkine (arseny.kapoulkine@gmail.com)
export type ExpMode = 'Separate' | 'SharedVector' | 'SharedComponent' | 'Clamped';
export const MeshoptEncoder: {
supported: boolean;
ready: ... |
5f18d0a30e7726cd93a2df363ca93fa85034c198aa15cb4187f355567c3f4c68 | TypeScript | 1,508 | 45 | // import * as d3 from "d3";
const d3 = require('d3');
class ColorScheme {
name: string;
value: Function;
type: string;
constructor(name: string, value: Function, type = 'continuous') {
this.name = name;
this.value = value;
this.type = type;
}
}
let colorSchemes: Array<ColorScheme> = [
new Co... |
9a13fa556a8bd39c937ada02eca047966415b6cef1f9fae5b26222e98da74249 | TypeScript | 1,573 | 57 | export const linearTransform = (d, r) => (v) =>
// https://gist.github.com/vectorsize/7031902
r[0] + (r[1] - r[0]) * ((v - d[0]) / (d[1] - d[0]));
export const ticks = (range, cscale = 1.0) => {
const sfig = Math.pow(10.0, Math.floor(Math.log10(range[1])));
const r: number[] = [],
lrange = [
Math.flo... |
c5ebb4255e02454305fe6e9d1c5a2f7342951297e79e2002dc7e815b3e3bcd56 | TypeScript | 1,804 | 81 | import { RefObject } from "react";
export type SubGroupedData = Map<string, Map<string, number[]>>;
export type ViolinPlotData = {
data: SubGroupedData;
innerKeys: Set<string>;
width: number;
domain: [number, number];
};
export type ViolinPlotMousedOverState = {
inner: string | null;
outer: string | null... |
eeb851550c579349ee91e8de5b52b42515a07c5f9f09f914ade0cafce0de192b | TypeScript | 1,838 | 69 | const CHANGE_EVENT_PREFIX = 'change:';
export class SocketModel {
socket_: any;
attachListeners_: any = [];
nameListeners_: Map<string, any> = new Map();
attach(socket: any) {
this.socket_ = socket;
this.attachListeners_.forEach((func: any) => {
func(this);
});
}
detach() {
this.soc... |
0106567d192becc7894a7be4cce986cbc4ef5a6bccb61be0e2f646315e84bd8d | TypeScript | 1,853 | 69 | // This file is part of meshoptimizer library and is distributed under the terms of MIT License.
// Copyright (C) 2016-2026, by Arseny Kapoulkine (arseny.kapoulkine@gmail.com)
export class Bounds {
centerX: number;
centerY: number;
centerZ: number;
radius: number;
coneApexX: number;
coneApexY: number;
coneApexZ... |
0c7fb8c2f3911fe0199f4ab535979d5d40fdc0006707e4c16927fb0ea227fd93 | TypeScript | 2,250 | 105 | import { ApolloClient, gql, InMemoryCache, useQuery } from "@apollo/client";
import { useMemo } from "react";
export type BiosampleEntry = {
dnase?: string | null;
h3k4me3?: string | null;
h3k27ac?: string | null;
ctcf?: string | null;
name: string;
lifeStage: string;
ontology: string;
sampleType: stri... |
05d0d8221c5e271692d357d3a06d0828168e4f217d4862a0ee0f81e4443cb74d | TypeScript | 2,253 | 110 | import {
AutocompleteProps,
BoxProps,
ButtonProps,
TextFieldProps,
} from "@mui/material";
// Props for the GenomeSearch component
export type GenomeSearchProps = Partial<
AutocompleteProps<Result, false, true, false, React.ElementType>
> & {
assembly: "GRCh38" | "mm10";
onSearchSubmit: (result: Result) ... |
44eb3725ba6dbe423c2f370726012bf417b9e9acbe502616a0f4ecf9addaeffe | TypeScript | 2,300 | 72 | import { GenomicRange } from "../GenePortal/AssociatedxQTL";
function compare(a: GenomicRange, b: GenomicRange): number {
const ca = +a
.chromosome!.replace(/chr/g, "")
.replace(/X/g, "23")
.replace(/Y/g, "24");
const cb = +b
.chromosome!.replace(/chr/g, "")
.replace(/X/g, "23")
.replace(/Y... |
053003fb43d6296a7d5a963d20f6ffc68f963a62f59215862616a49f6ac6fe31 | TypeScript | 2,327 | 94 | interface IndexedCollection extends Iterable<number> {
readonly length: number;
[index: number]: number;
}
// prettier-ignore
declare type mat2 =
| [number, number,
number, number]
| IndexedCollection;
// prettier-ignore
declare type mat2d =
| [number, number,
number, number,
number, n... |
79c0de71f35f3a6a73b34542a4f74f264d217abe0d16dbb7f485b8a55ec8fe81 | TypeScript | 2,392 | 109 | import { ApolloError, gql, useQuery } from "@apollo/client";
import { useMemo } from "react";
import {
TrackType,
DisplayMode,
LDTrackConfig,
useCustomData,
ManhattanTrackConfig,
} from "genomebrowser-test";
import {
BrowserStoreInstance,
DataStoreInstance,
ManhattanPoint,
} from "genomebrowser-test";
... |
5ee7a8c862d8b73f138365fbc50a20ccad8822c397e73c76664a7b9c158edab9 | TypeScript | 2,536 | 80 | // This file is part of meshoptimizer library and is distributed under the terms of MIT License.
// Copyright (C) 2016-2026, by Arseny Kapoulkine (arseny.kapoulkine@gmail.com)
export type SimplifierFlags = 'LockBorder' | 'Sparse' | 'ErrorAbsolute' | 'Prune' | 'Regularize' | 'Permissive' | 'RegularizeLight' | 'PreserveF... |
b30a62e58878a1e74023b7f7c42c442449d99ad1c905c5b4e59380b7d604cf48 | TypeScript | 2,649 | 65 | /**
* @license
* Copyright 2020 Google LLC. All Rights Reserved.
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* https://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by ... |
d3d8455595703dd80b84e57d5f60b3e15b7883ae70a2c4a28bb5858c41d1a913 | TypeScript | 2,949 | 83 | // An entry holds the key and value, and pointers to any older and newer entries.
interface Entry<K,V> {
key :K;
value :V;
}
export class LRUMap<K,V> {
// Construct a new cache object which will hold up to limit entries.
// When the size == limit, a `put` operation will evict the oldest entry.
//
// If `... |
ba83d2d47751de9aa9ec882bcbeb8e9e4895be5d08be4c1d7f9a0cb538724a63 | TypeScript | 3,116 | 76 | import { TrackList } from "../types";
export const DeepLearnedTracks: TrackList = {
"Adult brain bulk ATAC-seq": [
{
title: "VLPFC glia ATAC signal",
url: "gs://gcp.wenglab.org/projects/chrombpnet/psychencode/VLPFC_glia/predictions_VLPFC_glia_chrombpnet_nobias.bw",
},
{
title: "VLPFC ne... |
4bb7978278433ce99ca66a5df666e636b0e3875678362a29ba05a5e7eda0044c | TypeScript | 3,145 | 95 | import { createAction, PayloadAction } from '@reduxjs/toolkit'
import { call, put, takeEvery, select } from 'redux-saga/effects'
import fp from 'lodash/fp'
import * as api from '../api'
import { actions } from './actions'
import * as selectors from './selectors'
import { Worldline_t, worldline_id_t, Worldlines_t } fro... |
f7119119416643f42d0ab2353a91b7968edb91d5abbc1d82306dc77ef299668a | TypeScript | 3,744 | 113 | import { createSelector } from 'reselect'
import * as app_selectors from '../app/selectors'
import { idx_from_coord } from './helpers'
import { State_t } from '../app/model'
export const get_state = app_selectors.get_annotation_window_state
// Top level selectors
export const get_x = createSelector(get_state, s => s... |
779e833a878d3d1ad49778b10a6e2b6d74fd314d1cb44dc1506355be62e8d4e4 | TypeScript | 4,583 | 150 | import { call, put, takeEvery, takeLatest, select }
from 'redux-saga/effects'
import { createAction, PayloadAction } from '@reduxjs/toolkit'
import { actions } from './actions'
import { actions as annotation_window_actions ,
saga_actions as annotation_window_saga_actions }
from '../annotation_window'
import {saga... |
c4130c4e7b0d551d5829f08315871f7eefc83728d4e171d6418cb29d23989e2c | TypeScript | 4,671 | 181 | import { createSelector } from 'reselect'
import fp from 'lodash/fp'
import { Dictionary } from 'lodash'
import { annotation_id_t, Annotation_t } from './model'
import * as app_selectors from '../app/selectors'
import * as annotation_window_selectors from '../annotation_window/selectors'
import * as worldlines_selecto... |
8e77074ba3f9b4f23b4ce3c0e7c5b52e13e1369c075d4911ecca04c90a2016b7 | TypeScript | 5,024 | 212 | import { LRUMap } from '../third_party/lru'
import { AnnotationsState_t, Annotation_t, annotation_id_t } from '../annotations/model'
import { Worldline_t, Worldlines_t, worldline_id_t } from '../worldlines/model'
const image_cache = new LRUMap<string, Uint8ClampedArray>(5000)
const annotation_cache = new LRUMap<number... |
74d4935d774de2acabcf0a83df00a61773bb2cc2eaf116323abe7afe7579b083 | TypeScript | 5,426 | 200 | import { AnnotationWindowState_t as State_t, rpc_t } from './model'
import { createSlice, PayloadAction } from "@reduxjs/toolkit"
import { annotation_id_t, Annotation_t } from '../annotations/model'
import { worldline_id_t } from '../worldlines/model';
export const initialState: State_t = {
x: 0.5,
y: 0.5,
z: 0.... |
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