20 results found Sort:

seandavi
awesome-single-cell seandavi
995
3.2k
mit
248
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
793 commits to master branch, last one 16 days ago
macs3-project
MACS macs3-project
269
717
bsd-3-clause
48
MACS -- Model-based Analysis of ChIP-Seq
macs python atac-seq chip-seq dnase-seq peak-caller poisson-equation
Created 2011-03-02
1,675 commits to master branch, last one 21 days ago
maxplanck-ie
snakepipes maxplanck-ie
87
389
unknown
20
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
4,059 commits to master branch, last one 2 months ago
YuLab-SMU
ChIPseeker YuLab-SMU
76
230
unknown
20
:dart: ChIP peak Annotation, Comparison and Visualization
atac-seq chip-seq annotation comparison epigenetics epigenomics visualization
Created 2014-05-31
927 commits to devel branch, last one about a month ago
loosolab
TOBIAS loosolab
39
201
mit
16
Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal
atac-seq footprinting bioinformatics
Created 2019-09-04
424 commits to main branch, last one 8 days ago
nf-core
atacseq nf-core
119
193
mit
149
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 about a year ago
kundajelab
atac_dnase_pipelines kundajelab
79
164
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 5 years ago
GreenleafLab
chromVAR GreenleafLab
38
162
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 5 years ago
vanheeringen-lab
seq2science vanheeringen-lab
27
156
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 10 months ago
CostaLab
reg-gen CostaLab
30
106
other
11
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 about a year ago
LiuLabUB
HMMRATAC LiuLabUB
23
99
gpl-3.0
8
HMMRATAC peak caller for ATAC-seq data
atac-seq sequencing peak-caller peak-detection machine-learning
Created 2016-06-17
120 commits to master branch, last one about a month ago
tobiasrausch
ATACseq tobiasrausch
36
74
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 about a year ago
wbaopaul
scATAC-pro wbaopaul
24
73
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
393 commits to master branch, last one 21 days ago
reskejak
ATAC-seq reskejak
33
70
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
ParkerLab
ataqv ParkerLab
10
66
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
75 commits to master branch, last one 2 months ago
nf-core
differentialabundance nf-core
39
66
mit
150
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 7 months ago
igordot
sns igordot
28
64
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
173 commits to main branch, last one 2 months ago
epigen
atacseq_pipeline epigen
2
48
mit
3
Ultimate ATAC-seq Data Processing, Quantification and Annotation Snakemake Workflow and MrBiomics Module.
ngs bash python atac-seq pipeline workflow snakemake bioinformatics biomedical-data-science
Created 2021-03-22
172 commits to main branch, last one a day ago
sajuukLyu
Protocols-4pub sajuukLyu
13
48
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 about a year ago
junjunlab
BioSeqUtils junjunlab
2
30
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
80 commits to master branch, last one about a month ago