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20 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.

Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal

Seq2science ⭐ 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.

Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.

Dolphinnext ⭐ 92

A graphical user interface for distributed data processing of high throughput genomics

Nucleoatac ⭐ 78

nucleosome calling using ATAC-seq

Chromvar ⭐ 69

chromatin Variability Across Regions (of the genome!)

Scatac Pro ⭐ 64

A comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data

Atacseq_pipeline ⭐ 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.

Open_pipelines ⭐ 17

Pipelines for NGS data preprocessing by the Bock lab and friends

A toolkit for NGS analysis with Python

Cnnpeaks ⭐ 13

The ChIP-Seq peak calling algorithm using convolution neural networks

Pybedgraph ⭐ 13

A Python package for fast operations on 1-dimensional genomic signal tracks

Analysing Capture Seq Count Data

Workflows ⭐ 12

CWL based Bioinformatics Workflows

Enrichment_analysis ⭐ 10

A Snakemake workflow for performing genomic region set and gene set enrichment analyses using LOLA, GREAT, and GSEApy.

Cll Chromatin ⭐ 7

Data analysis scripts for Rendeiro et. al, 2016 (doi:10.1038/ncomms11938)

Sargasso disambiguates mixed-species high-throughput sequencing data.

R package for QC of enrichment based NGS assays. ChIP-seq, cut&run, ATAC-seq, etc.

Genome_tracks ⭐ 5

A Snakemake workflow for easy visualization of genome browser tracks of aligned BAM files powered by the wrapper gtracks for the package pyGenomeTracks.

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