19 results found Sort:

seandavi
awesome-single-cell seandavi
929
3.0k
mit
249
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
python analysis atac-seq cell-cycle clustering single-cell awesome-list rna-seq-data cell-clusters bioinformatics scrna-seq-data gene-expression cell-populations data-integration analysis-pipeline data-visualization rna-seq-experiments cell-differentiation dimensionality-reduction gene-expression-profiles
Created 2016-06-29
743 commits to master branch, last one 2 months ago
macs3-project
MACS macs3-project
273
687
bsd-3-clause
49
MACS -- Model-based Analysis of ChIP-Seq
macs python atac-seq chip-seq dnase-seq peak-caller poisson-equation
Created 2011-03-02
1,626 commits to master branch, last one 15 days ago
maxplanck-ie
snakepipes maxplanck-ie
85
372
mit
19
Customizable workflows based on snakemake and python for the analysis of NGS data
ngs hi-c rna-seq atac-seq chip-seq workflow snakemake bisulfite-sequencing
Created 2016-03-23
3,817 commits to master branch, last one about a month ago
YuLab-SMU
ChIPseeker YuLab-SMU
74
210
unknown
20
:dart: ChIP peak Annotation, Comparison and Visualization
atac-seq chip-seq annotation comparison epigenetics epigenomics visualization
Created 2014-05-31
884 commits to devel branch, last one 17 days ago
loosolab
TOBIAS loosolab
37
178
mit
16
Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal
atac-seq footprinting bioinformatics
Created 2019-09-04
384 commits to main branch, last one 5 months ago
nf-core
atacseq nf-core
115
163
mit
143
ATAC-seq peak-calling and QC analysis pipeline
nf-core atac-seq nextflow pipeline workflow chromatin-accessibiity
Created 2018-11-05
1,416 commits to master branch, last one 9 months ago
kundajelab
atac_dnase_pipelines kundajelab
81
160
bsd-3-clause
48
ATAC-seq and DNase-seq processing pipeline
atac-seq dnase-seq bioinformatics-pipeline
Created 2016-02-28
913 commits to master branch, last one 4 years ago
vanheeringen-lab
seq2science vanheeringen-lab
26
146
mit
6
Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Works equally easy with public as local data.
ngs sra fastq rna-seq atac-seq chip-seq pipeline snakemake workflows bioinformatics reproducible-research bioinformatics-pipeline
Created 2019-07-11
1,483 commits to master branch, last one 3 months ago
GreenleafLab
chromVAR GreenleafLab
36
142
other
21
chromatin Variability Across Regions (of the genome!)
r atac-seq dnase-seq bioinformatics
Created 2015-11-21
281 commits to master branch, last one 4 years ago
CostaLab
reg-gen CostaLab
30
101
other
12
Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.
ngs motif atac-seq chip-seq genomics dnase-seq footprinting bioinformatics motif-analysis differential-peak-calling
Created 2015-06-17
2,898 commits to master branch, last one 7 months ago
LiuLabUB
HMMRATAC LiuLabUB
22
97
gpl-3.0
8
HMMRATAC peak caller for ATAC-seq data
atac-seq sequencing peak-caller peak-detection machine-learning
Created 2016-06-17
114 commits to master branch, last one 4 years ago
tobiasrausch
ATACseq tobiasrausch
36
72
bsd-3-clause
7
Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)
atac-seq chromatin sequencing peak-detection atac-seq-pipeline nucleosome-positioning next-generation-sequencing
Created 2016-09-05
187 commits to main branch, last one 10 months ago
wbaopaul
scATAC-pro wbaopaul
24
65
mit
6
A comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data
atac-seq pipeline single-cell bioinformatics chromatin-accessibiity
Created 2019-05-21
385 commits to master branch, last one 11 months ago
ParkerLab
ataqv ParkerLab
10
63
gpl-3.0
8
A toolkit for QC and visualization of ATAC-seq results.
tool atac-seq software visualization quality-control
Created 2015-11-10
72 commits to master branch, last one about a year ago
reskejak
ATAC-seq reskejak
30
62
unknown
4
Basic workflow for ATAC-seq analysis
r unix shell atac-seq
Created 2018-03-30
58 commits to master branch, last one 2 years ago
igordot
sns igordot
27
61
mit
8
Analysis pipelines for genomic sequencing data
dna nyu wes wgs rrbs wgbs rna-seq analysis atac-seq genomics illumina pipeline sequencing bioinformatics
Created 2016-08-24
166 commits to main branch, last one 3 days ago
nf-core
differentialabundance nf-core
27
46
mit
143
Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq
gsea limma shiny deseq2 nf-core rna-seq atac-seq chip-seq nextflow pipeline workflow microarray differential-abundance differential-expression
Created 2022-10-12
1,105 commits to master branch, last one 23 days ago
sajuukLyu
Protocols-4pub sajuukLyu
13
45
gpl-3.0
3
Multi-omics analysis protocols by Lyu.
wgbs rna-seq atac-seq chip-seq
Created 2021-03-08
49 commits to main branch, last one 9 months ago
junjunlab
BioSeqUtils junjunlab
1
26
other
2
Extract Sequence from Genome According to Annotation File
gtf hic genome atac-seq chip-seq merip-seq transcript coverage-plot
Created 2023-03-03
76 commits to master branch, last one 7 months ago