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Add IDR analysis

feature-requestRequest to add new functionalityRequest to add new functionality

Status: Open.

#87 In nf-core/chipseq;

· drpatelh opened on May 30, 2019

Merged biological replicates

Status: Open.

#213 In nf-core/chipseq;

· ryanmboileau opened on May 3, 2021

Output bigwigs with macs2 p-value signal for every base-pair

feature-requestRequest to add new functionalityRequest to add new functionality

Status: Open.

#251 In nf-core/chipseq;

· Al-Murphy opened on Feb 3, 2022

Find test dataset where PRESEQ doesn't fail

enhancement

Status: Open.

#276 In nf-core/chipseq;

· drpatelh opened on May 9, 2022

Implementation of Nucleosome and Protein Occupancy analysis

feature-requestRequest to add new functionalityRequest to add new functionality

help wantedExtra attention is neededExtra attention is needed

Status: Open.

#289 In nf-core/chipseq;

· snardeli opened on Jul 27, 2022

Spike ins normalization

enhancement

Status: Open.

#321 In nf-core/chipseq;

· EmanuelSoda opened on Oct 28, 2022

Add --only_step options

enhancement

Status: Open.

#337 In nf-core/chipseq;

· IStevant opened on Mar 8, 2023

Adjust x-axis to start at 1 for custom phantompeakqualtools NSC plot

enhancement

Status: Open.

#441 In nf-core/chipseq;

· pontushojer opened on Dec 17, 2024

Output .bed file not found in the MACS2 folder

enhancement

Status: Open.

#448 In nf-core/chipseq;

· GopishankarThirumoorthy opened on Feb 3, 2025

Can we do chip seq analysis using nextflow without input sample?

enhancement

Status: Open.

#452 In nf-core/chipseq;

· autumnfe79 opened on Mar 6, 2025

Enable the use of CSI bam index

enhancement

Status: Open.

#454 In nf-core/chipseq;

· JoseEspinosa opened on Mar 12, 2025

Call peak without chip-seq input control.

enhancement

Status: Open.

#457 In nf-core/chipseq;

· ljw20180420 opened on Mar 21, 2025

Add minimum_alignment_q_score parameter for MAPQ filtering (similar to nf-core/cutandrun)

enhancement

Status: Open.

#463 In nf-core/chipseq;

· wanisajad opened on May 16, 2025

Switch local/module GTF2BED to nf-core/module BEDOPS_GTF2BED

enhancement

Status: Open.

#494 In nf-core/chipseq;

· Kevin-Brockers opened on Mar 20, 2026

Port bedtools_genomecov from local to nf-core module

improve-behaviourOptimise code without adding functionalityOptimise code without adding functionality

Status: Open.

Task

#469 In nf-core/chipseq;

· FloWuenne opened on Jun 24, 2025