26 skills found
macs3-project / MACSMACS -- Model-based Analysis of ChIP-Seq
GreenleafLab / ChromVARchromatin Variability Across Regions (of the genome!)
kundajelab / Atac Dnase PipelinesATAC-seq and DNase-seq processing pipeline
CostaLab / Reg GenRegulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.
inutano / Chip AtlasChIP-Atlas: Browse and analyze all public ChIP/DNase-seq data on your browser
kundajelab / PhantompeakqualtoolsThis package computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to obtain robust estimates of the predominant fragment length or characteristic tag shift values in these assays.
SUwonglab / PECAPECA is a software for inferring context specific gene regulatory network from paired gene expression and chromatin accessibility data
jpiper / PyDNasePython module for the easy handling and analysis of DNase-seq data
gtrichard / DeepStatsdeepStats: a stastitical toolbox for deeptools and genomic signals
uci-cbcl / EXTREMEAn online EM implementation of the MEME model for fast motif discovery in large ChIP-Seq and DNase-Seq Footprinting data
WeiqiangZhou / BIRDBig data Regression for predicting DNase I hypersensitivity
kernco / Functional AnnotationPipeline for functional annotation of genomes by integrating data from RNA-seq, ChIP-seq, DNase-seq, etc.
slowkow / CENTIPEDE.tutorial:bug: How to use CENTIPEDE to determine if a transcription factor is bound.
Duke-GCB / GGR CwlCWL tools and workflows for GGR
c-guzman / Cipher Workflow PlatformA data processing platform for ChIP-seq, RNA-seq, MNase-seq, DNase-seq, ATAC-seq and GRO-seq datasets. Please ignore information on cipher.readthedocs.io, it is currently out of date. Follow information in README.
ENCODE-DCC / Dnase PipelineENCODE DNase-seq pipeline essentials for running on dnanexus.
aslihankarabacak / FootprintPipelinePipeline to find transcription factor footprints in DNase-seq or ATAC-seq datasets
YosefLab / EpitomePipeline for predicting ChIP-seq peaks in novel cell types using chromatin accessibility
eggduzao / OlympusA unified framework for discovering, analyzing, integrating, and visualizing regulatory motifs and transcription factor binding sites across bulk, single-cell, and long-read sequencing modalities.
ajank / RomulusRomulus: Robust multi-state identification of transcription factor binding sites from DNase-seq data
