Ecosyste.ms: Issues

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GitHub / macs3-project/MACS issues and pull requests

#681 - Q: the likelihood of bdgdiff

Issue - State: open - Opened by BenxiaHu about 1 month ago
Labels: General Question

#679 - Q: Haplotype genomes have no peak

Issue - State: open - Opened by bigshark12345 about 2 months ago
Labels: General Question

#678 - Expose the "peaks" field in BroadPeakIO

Pull Request - State: closed - Opened by kaizhang about 2 months ago - 1 comment

#677 - Q: AssertionError: No proper d can be found! Tweak --mfold?

Issue - State: open - Opened by nanu23333 about 2 months ago
Labels: General Question

#674 - Docs: "Install from source" guide is broken

Issue - State: closed - Opened by aowenson-imm 2 months ago - 1 comment
Labels: Bug Report

#673 - Q: There's a huge difference between my peak number and the bio company's peak number

Issue - State: open - Opened by bigshark12345 2 months ago - 2 comments
Labels: General Question

#672 - Bug: NameError: name 'BedGraphIO' is not defined. Did you mean: 'bedGraphIO'?

Issue - State: open - Opened by acv21 2 months ago - 1 comment
Labels: Bug Report

#671 - Q: MACS3 hmmratac for single-cell ATAC-seq

Issue - State: open - Opened by acv21 2 months ago - 3 comments
Labels: General Question

#670 - Q: gappedPeak instead of narrow peak on HMMRATAC output

Issue - State: open - Opened by jffpviana 3 months ago - 3 comments
Labels: General Question

#669 - Q: Filtering blacklisted regions when using macs3 hmmeratac

Issue - State: open - Opened by eggrandio 3 months ago - 1 comment
Labels: General Question

#668 - Feat/macs3/fragmentfile

Pull Request - State: closed - Opened by taoliu 3 months ago

#667 - Bug: Overflow error when using Poisson law for bdgcmp

Issue - State: open - Opened by callum-b 3 months ago - 3 comments
Labels: Bug Report

#666 - Bug: Runtime error pybind11::handle::inc_ref() PyGILState_Check() failure.

Issue - State: open - Opened by Kiliankleemann 3 months ago - 1 comment
Labels: Bug Report

#665 - Feat: Multiprocessing for calling peaks (1 process per chromosome)

Issue - State: open - Opened by jeanmonet 3 months ago
Labels: Feature Request

#664 - Feat/macs3/python style cython (1st)

Pull Request - State: closed - Opened by taoliu 3 months ago

#663 - Bug: Illegal instruction (core dumped)

Issue - State: open - Opened by marinafloresp 3 months ago - 1 comment
Labels: Bug Report

#662 - Feat/macs3/reformat pyproject

Pull Request - State: closed - Opened by taoliu 4 months ago

#661 - Q: does BAMPE format require a name-sorted BAM or coordinate-sorted bam or it does not matter?

Issue - State: closed - Opened by sotuamax 4 months ago - 2 comments
Labels: General Question

#658 - Bug: Are requirements stated correctly?

Issue - State: closed - Opened by outpaddling 4 months ago - 2 comments
Labels: Bug Report

#657 - Doc/macs3/3.0.2 for v3.0.2 release

Pull Request - State: closed - Opened by taoliu 4 months ago
Labels: v3

#656 - Q: What parameters should I need to tweak for viral ChipSeq

Issue - State: open - Opened by Rohit-Satyam 5 months ago - 1 comment
Labels: General Question

#655 - Bug: Multiple errors trying to install MACS2 on a venv

Issue - State: closed - Opened by fionafitzz 5 months ago - 1 comment
Labels: Bug Report

#654 - Better cutoff levels control for bdgcallpeak cutoff-analysis

Issue - State: open - Opened by callum-b 6 months ago - 1 comment
Labels: Feature Request

#653 - MACS3 callpeak does not create UCSC Browser ready peak files

Issue - State: closed - Opened by callum-b 6 months ago - 1 comment
Labels: Bug Report

#652 - Q: using macs3 to detect peaks on long-read readings

Issue - State: open - Opened by MJoseMo 7 months ago
Labels: General Question

#651 - Feat: Add --call-summits option in MACS3 bdgpeakcall?

Issue - State: open - Opened by alicewang19 7 months ago
Labels: Feature Request

#649 - Bug: OverflowError when running hmmratac

Issue - State: open - Opened by atj31 7 months ago
Labels: Bug Report

#648 - Q: How to use HMMRATAC to give us a narrow peak file and have signalValue, p and q-value ?

Issue - State: open - Opened by MinaMyr 7 months ago - 1 comment
Labels: General Question

#646 - Setting cut-off when using logFE bigWig files from bdgcmp

Issue - State: open - Opened by manjumoorthy95 8 months ago
Labels: General Question

#645 - Feat/macs3/narrowpeak

Pull Request - State: closed - Opened by taoliu 8 months ago

#644 - Q: impact of sequencing throughput on peak calling

Issue - State: closed - Opened by SplitInf 8 months ago - 4 comments
Labels: General Question

#643 - Bug: Callvar throws an error when run on broadPeak file

Issue - State: open - Opened by LinearParadox 9 months ago - 15 comments
Labels: Bug Report

#642 - Documentation update and refine cutoff-analysis for `hmmratac`

Pull Request - State: closed - Opened by taoliu 9 months ago

#639 - Q: how to use MACS3 for ATAC seq with "himmratac" option?

Issue - State: open - Opened by kbarrr 9 months ago - 2 comments
Labels: General Question

#638 - Q: HMMRATAC reproducibility

Issue - State: open - Opened by igordot 10 months ago - 2 comments
Labels: General Question

#637 - Bug: undefined symbol: __pow_finite

Issue - State: open - Opened by jowodo 10 months ago - 3 comments
Labels: Bug Report

#637 - Bug: undefined symbol: __pow_finite

Issue - State: open - Opened by jowodo 10 months ago - 1 comment
Labels: Bug Report

#636 - Q: HMMRATAC producing too many peaks

Issue - State: open - Opened by igordot 10 months ago - 10 comments
Labels: General Question

#636 - Q: HMMRATAC producing too many peaks

Issue - State: open - Opened by igordot 10 months ago - 9 comments
Labels: General Question

#635 - Feat/macs3/hmm poisson

Pull Request - State: closed - Opened by philippadoherty 10 months ago - 1 comment

#634 - Feat: Built-in scoring for HMMRATAC

Issue - State: open - Opened by mrendleman 11 months ago - 1 comment
Labels: Feature Request

#633 - Q: HMMRATAC output and options for _summit.bed

Issue - State: open - Opened by kawairine 11 months ago - 1 comment
Labels: General Question

#632 - Use trusted publishing to upload package to pypi

Pull Request - State: closed - Opened by taoliu 11 months ago

#631 - Feat/macs3/hmmlearn0.3.2

Pull Request - State: closed - Opened by taoliu 11 months ago

#628 - Feat: Reduction of memory consumption

Issue - State: open - Opened by diego-rt 11 months ago - 3 comments
Labels: Feature Request

#627 - Feat/macs3/unittest hmm

Pull Request - State: open - Opened by taoliu 11 months ago

#627 - Feat/macs3/unittest hmm

Pull Request - State: open - Opened by taoliu 11 months ago - 1 comment

#626 - Feat: Enhanced clarification of the specific definition of BEDPE as used by MACS

Issue - State: open - Opened by kalavattam 11 months ago - 1 comment
Labels: Feature Request

#626 - Feat: Enhanced clarification of the specific definition of BEDPE as used by MACS

Issue - State: open - Opened by kalavattam 11 months ago - 1 comment
Labels: Feature Request

#625 - Feat/macs3/output vers libs ga

Pull Request - State: closed - Opened by taoliu 11 months ago

#625 - Feat/macs3/output vers libs ga

Pull Request - State: closed - Opened by taoliu 11 months ago

#624 - fix SyntaxWarning by marking a regex as such

Pull Request - State: closed - Opened by mr-c 11 months ago - 1 comment

#624 - fix SyntaxWarning by marking a regex as such

Pull Request - State: closed - Opened by mr-c 11 months ago - 1 comment

#623 - explictly use Python version 3

Pull Request - State: closed - Opened by mr-c 11 months ago - 1 comment

#622 - Release/macs3/3.0.1

Pull Request - State: closed - Opened by taoliu 11 months ago

#621 - Q: conversion of output files to UCSC track hub format?

Issue - State: open - Opened by maximilianh 11 months ago - 1 comment
Labels: General Question

#620 - patch hmmlearn, fix dependencies

Pull Request - State: closed - Opened by taoliu 11 months ago

#618 - Doc/macs3/sphinx migration -> test_peak_overlap

Pull Request - State: closed - Opened by taoliu 11 months ago

#617 - What is the difference between "absolute peak summit" and "summit position" in narrowPeak format?

Issue - State: open - Opened by mcsimenc 12 months ago - 1 comment
Labels: General Question

#616 - Bug: pip install error: subprocess-exited-with-error

Issue - State: open - Opened by ferygood 12 months ago - 1 comment
Labels: Bug Report

#616 - Bug: pip install error: subprocess-exited-with-error

Issue - State: closed - Opened by ferygood 12 months ago - 2 comments
Labels: Bug Report

#615 - Bug: test suite failure in MACS 3.0.0

Issue - State: closed - Opened by tillea 12 months ago - 18 comments
Labels: Bug Report

#614 - Q: Defining the bin size when generating bedgraphs.

Issue - State: open - Opened by rikrdo89 about 1 year ago
Labels: General Question

#613 - Q: Is there a way to specify blacklisted regions in MACS2?

Issue - State: open - Opened by rikrdo89 about 1 year ago
Labels: General Question

#612 - remove cython from setup.py requirements

Pull Request - State: closed - Opened by taoliu about 1 year ago

#611 - fix labels for signals

Pull Request - State: closed - Opened by philippadoherty about 1 year ago - 1 comment

#610 - Mention alternative installation methods in install guide

Issue - State: open - Opened by outpaddling about 1 year ago
Labels: Feature Request

#609 - Bug: Test scripts failing

Issue - State: closed - Opened by outpaddling about 1 year ago - 1 comment
Labels: Bug Report

#608 - Q: lambda estimation

Issue - State: open - Opened by pegahtak about 1 year ago
Labels: General Question

#607 - Q: What context should be specified for the 'gsize' option with killifish mapping data?

Issue - State: open - Opened by LoganLHJ about 1 year ago - 1 comment
Labels: General Question

#606 - Bug: cython is required at build time but not install time

Issue - State: closed - Opened by tillea about 1 year ago - 2 comments
Labels: Bug Report

#605 - Bug: HMMRATAC --save-digested outputs four identical signal tracks

Issue - State: closed - Opened by mrendleman about 1 year ago
Labels: Bug Report

#604 - Q: question about the libmvec.so.1 error.

Issue - State: open - Opened by Simple53 about 1 year ago - 5 comments
Labels: General Question

#603 - Q: about the 'max-gap 'parameter

Issue - State: open - Opened by liuyu988 about 1 year ago
Labels: General Question

#601 - Q: the questions about calling broad peaks

Issue - State: open - Opened by liuyu988 about 1 year ago
Labels: General Question

#600 - Doc/macs3/jekyll equations

Pull Request - State: closed - Opened by philippadoherty about 1 year ago - 1 comment

#599 - Use of IDR after running MACS3 for ATAC-seq data

Issue - State: closed - Opened by OrangeyO2 about 1 year ago - 2 comments
Labels: General Question

#598 - Bug: python3.12 incompatible due to numpy<1.24 restriction

Issue - State: closed - Opened by jowodo about 1 year ago - 7 comments
Labels: Bug Report

#598 - Bug: python3.12 incompatible due to numpy<1.24 restriction

Issue - State: open - Opened by jowodo about 1 year ago
Labels: Bug Report

#597 - MACS3 3.0.0 official release with docs updated

Pull Request - State: open - Opened by taoliu about 1 year ago

#597 - MACS3 3.0.0 official release with docs updated

Pull Request - State: closed - Opened by taoliu about 1 year ago

#596 - Bug: BEDPE Format input for hmmratac

Issue - State: closed - Opened by bcantarel over 1 year ago - 3 comments
Labels: Bug Report

#595 - Bug:

Issue - State: open - Opened by XuJahcenia over 1 year ago - 1 comment
Labels: Bug Report

#594 - Bug: `LINK : fatal error LNK1181: cannot open input file 'm.lib'`

Issue - State: closed - Opened by danli349 over 1 year ago - 2 comments
Labels: Bug Report

#593 - hmmratac adjust means and standard deviation

Issue - State: open - Opened by LinearParadox over 1 year ago - 5 comments
Labels: Bug Report

#592 - gapped peak column 13 through 15

Issue - State: open - Opened by ketakibhide over 1 year ago - 1 comment
Labels: General Question

#592 - gapped peak column 13 through 15

Issue - State: open - Opened by ketakibhide over 1 year ago - 1 comment
Labels: General Question

#591 - Bug:

Issue - State: closed - Opened by david2905 over 1 year ago - 2 comments
Labels: Bug Report

#591 - Bug:

Issue - State: open - Opened by david2905 over 1 year ago - 1 comment
Labels: Bug Report

#590 - macs2: remove pip and wheel from build dependencies

Pull Request - State: closed - Opened by tjni over 1 year ago - 1 comment

#590 - macs2: remove pip and wheel from build dependencies

Pull Request - State: closed - Opened by tjni over 1 year ago - 1 comment

#589 - remove pip and wheel from build dependencies

Pull Request - State: closed - Opened by tjni over 1 year ago - 2 comments

#589 - remove pip and wheel from build dependencies

Pull Request - State: closed - Opened by tjni over 1 year ago - 2 comments

#587 - macs use the log() math function, but doesn't always link with libm.so.

Pull Request - State: closed - Opened by mr-c over 1 year ago - 1 comment