Biocview "DifferentialPeakCalling"

GenoGAM

A GAM based framework for analysis of ChIP-Seq data

gstricker/GenoGAM

A GAM based framework for analysis of ChIP-Seq data

gstricker/fastGenoGAM

A GAM based framework for analysis of ChIP-Seq data

vallotlab/ChromSCape

Analysis of single-cell epigenomics datasets with a Shiny App

ChromSCape

Analysis of single-cell epigenomics datasets with a Shiny App

lcolladotor/derfinder

Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach

derfinder

Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach

selinj/chromswitch

An R package to detect chromatin state switches from epigenomic data

chromswitch

An R package to detect chromatin state switches from epigenomic data

sjessa/chromswitch

An R package to detect chromatin state switches from epigenomic data

LTLA/csaw

ChIP-Seq Analysis with Windows

csaw

ChIP-Seq Analysis with Windows

CSSQ

Chip-seq Signal Quantifier Pipeline

chromstaR

Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data

ataudt/chromstaR

Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data

ManchesterBioinference/Motif2Site

Detect binding sites from motifs and ChIP-seq experiments, and compare binding sites across conditions

DiffBind

Differential Binding Analysis of ChIP-Seq Peak Data

tengmx/ComplexDiff

Differential Binding Estimation for Protein Complexes

GabrielHoffman/decorate

Differential Epigenetic Coregulation Test

regionReport

Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results

leekgroup/regionReport

Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results

GreyListChIP

Grey Lists -- Mask Artefact Regions Based on ChIP Inputs

IWTomics

Interval-Wise Testing for Omics Data

marziacremona/IWTomics

Interval-Wise Testing for Omics Data

LTLA/metapod

Meta-Analyses on P-Values of Differential Analyses

imbbLab/normr

Normalization and difference calling in ChIP-seq data

your-highness/normR

Normalization and difference calling in ChIP-seq data

normr

Normalization and difference calling in ChIP-seq data

Bohdan-Khomtchouk/geneXtendeR_keepme

Optimized Functional Annotation Of ChIP-seq Data

Bohdan-Khomtchouk/geneXtendeR

Optimized Functional Annotation Of ChIP-seq Data

geneXtendeR

Optimized Functional Annotation Of ChIP-seq Data

ZW-xjtlu/exomePeak2

Peak Calling and differential analysis for MeRIP-Seq

ZhenWei10/exomePeak2

Peak Calling and differential analysis for MeRIP-Seq

jianhong/diffPeaks

Quantifying Differential Features

MMDiff2

Statistical Testing for ChIP-Seq data sets

dhelekal/mmdiff3

Statistical Testing for ChIP-Seq data sets