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Search results for atac seq
atac-seq
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62 search results found
Awesome Single Cell
⭐
2,784
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
Macs
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684
MACS -- Model-based Analysis of ChIP-Seq
Snakepipes
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359
Customizable workflows based on snakemake and python for the analysis of NGS data
Chipseeker
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204
🎯 ChIP peak Annotation, Comparison and Visualization
Tobias
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162
Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal
Atacseq
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145
ATAC-seq peak-calling and QC analysis pipeline
Atac_dnase_pipelines
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135
ATAC-seq and DNase-seq processing pipeline
Seq2science
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132
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.
Reg Gen
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96
Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.
Scatac Benchmarking
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92
Benchmarking computational single cell ATAC-seq methods
Dolphinnext
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92
A graphical user interface for distributed data processing of high throughput genomics
Nucleoatac
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78
nucleosome calling using ATAC-seq
Chromvar
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69
chromatin Variability Across Regions (of the genome!)
Scatac Pro
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64
A comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data
Atacseq
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64
Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)
Ataqv
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62
A toolkit for QC and visualization of ATAC-seq results.
Hmmratac
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49
HMMRATAC peak caller for ATAC-seq data
Protocols 4pub
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40
Multi-omics analysis protocols by Lyu.
Pyflow Atacseq
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37
ATAC-seq snakemake pipeline
Peca
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35
PECA is a software for inferring context specific gene regulatory network from paired gene expression and chromatin accessibility data
Differentialabundance
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34
Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq
Wiggleplotr
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28
A small R package to make sequencing read coverage plots in R.
Deepstats
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27
deepStats: a stastitical toolbox for deeptools and genomic signals
Atacseq_pipeline
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25
Ultimate ATAC-seq Data Processing & Quantification Workflow. A Snakemake implementation of the BSF's ATAC-seq Data Processing Pipeline extended by downstream quantification and annotation steps using bash and Python.
Irena
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24
R package IReNA
Maxatac
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24
Transcription Factor Binding Prediction from ATAC-seq and scATAC-seq with Deep Neural Networks
Scasat
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24
Scasat is a single cell ATAC-seq preprocessing and analysis pipeline
Biosequtils
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21
Extract Sequence from Genome According to Annotation File
Bioinf545
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20
ATAC-seq lab for BIOINF545
Atac Seq
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19
Basic workflow for ATAC-seq analysis
Ggr Cwl
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19
CWL tools and workflows for GGR
Gchromvar
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18
Cell type specific enrichments using finemapped variants and quantitative epigenetic data
Atactk
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18
A toolkit for working with ATAC-seq data.
Open_pipelines
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17
Pipelines for NGS data preprocessing by the Bock lab and friends
Pumatac
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16
Pipeline for Universal Mapping of ATAC-seq
Sckinetics
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15
Code for scKINETICS (ISMB 2023)
Atacproc
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15
ATAC-seq processing pipeline
Cnnpeaks
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13
The ChIP-Seq peak calling algorithm using convolution neural networks
Pybedgraph
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13
A Python package for fast operations on 1-dimensional genomic signal tracks
Toolkit
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13
A toolkit for NGS analysis with Python
Alps
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12
AnaLysis routines for ePigenomicS data.
Atacr
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12
Analysing Capture Seq Count Data
Workflows
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12
CWL based Bioinformatics Workflows
Couplednmf
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11
Coupled clustering of single cell genomic data
Cinar
⭐
10
A differential and enrichment analyses pipeline for bulk ATAC-seq (and RNA-seq)
Atacflow
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10
An ATAC-seq pipeline wrapped in NextFlow that can be run by Jupyter
Proatac
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10
Preprocessing pipeline for (sc)ATAC data
Cellatac
⭐
10
Sanger Cellular Genetics single-cell ATAC-seq pipeline.
Enrichment_analysis
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10
A Snakemake workflow for performing genomic region set and gene set enrichment analyses using LOLA, GREAT, and GSEApy.
Bindvae
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8
Variational Auto Encoders for learning binding signatures of transcription factors
Epitome
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8
Pipeline for predicting ChIP-seq peaks in novel cell types using chromatin accessibility
Debpeak
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8
DEbPeak - Analyze and integrate multi-omics to unravel the regulation of gene expression.
Scatac Mouse Human Control
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8
Mouse / human control of cross-contaminations in single-cell ATAC-seq on Fluidigm C1
Multirepmacschipseq
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7
Multiple-replica multiple-condition Macs2 ChIPSeq wrapper
Fluentgenomics
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7
plyranges and tximeta case study
Cll Chromatin
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7
Data analysis scripts for Rendeiro et. al, 2016 (doi:10.1038/ncomms11938)
Sargasso
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6
Sargasso disambiguates mixed-species high-throughput sequencing data.
Bioinf525
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6
ATAC-seq lab for BIOINF525
As_analysis
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5
A complete Snakemake pipeline for detecting allele specific expression
Genome_tracks
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5
A Snakemake workflow for easy visualization of genome browser tracks of aligned BAM files powered by the wrapper gtracks for the package pyGenomeTracks.
Ssvqc
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5
R package for QC of enrichment based NGS assays. ChIP-seq, cut&run, ATAC-seq, etc.
Rocco
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5
Robust Open Chromatin Detection via Convex Optimization: Consensus Peak Calling for ATAC-seq
1-62 of 62 search results
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