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peak-calling

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nf-core /chipseq

ChIP-seq peak-calling, QC and differential analysis pipeline.

workflow pipeline nextflow chip chip-seq macs2 nf-core chromatin-immunoprecipitation peak-calling

UpdatedMar 12, 2025
Nextflow

nf-core /clipseq

CLIP sequencing analysis pipeline for QC, pre-mapping, genome mapping, UMI deduplication, and multiple peak-calling options.

workflow pipeline nextflow clip clip-seq nf-core peak-calling rna-rbp-interactions

UpdatedMar 9, 2025
Nextflow

odb9402 /CNNPeaks

The ChIP-Seq peak calling algorithm using convolution neural networks

bioinformatics tensorflow gpu docker-image chip-seq atac-seq nvidia-docker convolutional-neural-network samtools cnn-model ngs-analysis peak-calling progressbar2

UpdatedJan 18, 2021
Python

HuntsmanCancerInstitute /MultiRepMacsChIPSeq

Multiple-replica multiple-condition Macs2 ChIPSeq wrapper

chip-seq atac-seq chromatin macs2 peak-calling

UpdatedJan 30, 2025
Perl

nanxstats /oneclust

🥇 Maximum homogeneity clustering for one-dimensional data

feature-engineering clustering-algorithm peak-calling homogeneity univariate-data

UpdatedApr 26, 2024
R

RenneLab /CnR-flow

CUT&RUN-Flow, A Nextflow pipeline for QC, tag trimming, normalization, and peak calling for data from CUT&RUN experiments.

genomics nextflow chip-seq-pipelines cutandrun-seq peak-calling cutandrun cutrun

UpdatedApr 5, 2022
Nextflow

skchronicles /PeakCalling

Benchmarking ChIP-seq peak callers

music gem chip-seq sicer macs2 peak-analysis peak-calling broad-peaks narrow-peaks dfilter pepr

UpdatedDec 11, 2018
Python

OpenOmics /chrom-seek

An awesome set of epigenetic pipelines for bulk cfChip-seq, ChIP-seq, and ATAC-seq

quality-control annotation chip-seq atac-seq bulk cell-free-dna peak-calling differential-accessibility differential-binding

UpdatedMar 17, 2025
Python

OpenOmics /cfChIP-seek

cell-free ChIP-seq pipeline

quality-control snakemake chip-seq cell-free-dna peak-calling peak-annotation cell-type-deconvolution

UpdatedFeb 7, 2024
Python

JetBrains-Research /chipseq-smk-pipeline

ChIP-Seq processing pipeline on snakemake

visualization quality-control snakemake pipeline chip-seq atac-seq peak-calling

UpdatedMar 1, 2025
Python

jawa23bio /ATAC-Seq

Comprehensive analysis pipeline for ATAC-seq data including QC, alignment, peak calling, annotation, motif analysis, and gene enrichment. Delivers key insights and reproducible results for chromatin accessibility studies.

motif-analysis peak-calling chromatin-accessibiity atac-seq-pipeline peak-annotation

UpdatedMay 14, 2024
HTML

AntoinePassemiers /ChIP-seq-Peak-Caller

Peak Calling algorithm for Chromatin-immunoprecipitation sequencing (ChIP-seq) data

chip-seq peak-calling

UpdatedMay 12, 2019
Python

meekrob /spp

SPP - R package for analysis of ChIP-seq and other functional sequencing data

hpc chip-seq peak-calling onishlab

UpdatedJan 25, 2018
C++

vonMeyennLab /nf_peakcalling

A Nextflow pipeline to perform peak calling of ChIP-seq, ATAC-seq or CUT&Tag sequencing data.

peak-calling nextflow-pipeline

UpdatedFeb 25, 2025
Nextflow

neurogenomics /PeakyFinders

R package for mining, calling, and importing epigenomic peaks.

r genomics encode r-package epigenomics gene-expression-omnibus peak-calling

UpdatedOct 2, 2024
R

deeprob /biopeaker

Peak classification with Deep Learning

deep-learning peak-calling sequence-annotation motif-prediction

UpdatedJun 28, 2023
Python

dansta0804 /TF_analysis

Repozitorijoje saugomi failai, implementuojantys R Shiny aplikaciją ir leidžiantys vertinti įkeltų genominių duomenų kokybę bei vykdyti biologines analizes.

r genome-annotation chip-seq transcription-factor-binding pwm shinydashboard genomic-regions homo-sapiens peak-calling mus-musculus

UpdatedJun 14, 2023
R

stjude-biohackathon /peakPeekeR

Peak calling optimization via real time results assessment and interactive parameter adjustment.

shiny chip-seq atac-seq macs macs2 peak-calling cutandrun cutandtag genrich peak-callers sicer2

UpdatedApr 29, 2022
R

JetBrains-Research /washu

Reproducible and scalable technical pipelines for ChIP-Seq and RNA-Seq processing

visualization bash rna-seq pipeline analysis parallel-computing chip-seq qsub qc peak-calling

UpdatedMar 13, 2023
Shell

petrokvitka /Footprints_extraction

A small script to find peaks from the .bigWig file and output them in a .bed file.

signal bigwig footprint peak-detection peak-calling

UpdatedFeb 14, 2019
Python

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