macs3-project/MACS

Issues

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

  #652 opened 5 days ago by MJoseMo
  0

• Feat: Add --call-summits option in MACS3 bdgpeakcall?

  #651 opened 12 days ago by alicewang19
  0

• Number of de-duplicated reads indicated by filterdup log does not match number of lines in output BED file.

  #650 opened 18 days ago by callum-b
  0

• Bug: OverflowError when running hmmratac

  #649 opened 19 days ago by atj31
  0

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

  #648 opened 25 days ago by MinaMyr
  1

• Q: impact of sequencing throughput on peak calling

  #644 opened a month ago by SplitInf
  4

• Setting cut-off when using logFE bigWig files from bdgcmp

  #646 opened a month ago by manjumoorthy95
  0

• Bug: Callvar throws an error when run on broadPeak file

  #643 opened 2 months ago by LinearParadox
  15

• Q: how to use MACS3 for ATAC seq with "himmratac" option?

  #639 opened 3 months ago by kbarrr
  3

• Q: HMMRATAC producing too many peaks

  #636 opened 3 months ago by igordot
  10

• Bug: undefined symbol: __pow_finite

  #637 opened 3 months ago by jowodo
  3

• Q: HMMRATAC reproducibility

  #638 opened 3 months ago by igordot
  2

• Feat: Built-in scoring for HMMRATAC

  #634 opened 4 months ago by mrendleman
  1

• gapped peak column 13 through 15

  #592 opened 10 months ago by ketakibhide
  1

• Q: HMMRATAC output and options for _summit.bed

  #633 opened 4 months ago by kawairine
  1

• Q: Why peak region didn't appear with lower q-value than cut-off

  #586 opened a year ago by khsjh
  1

• Feat: Reduction of memory consumption

  #628 opened 4 months ago by diego-rt
  3

• Feat: Enhanced clarification of the specific definition of BEDPE as used by MACS

  #626 opened 4 months ago by kalavattam
  1

• Two lines in Signal/PeakVariants.pyx causing installation errors

  #572 opened 4 months ago by franciskim-yonsei
  1

• Bug: cython is required at build time but not install time

  #606 opened 4 months ago by tillea
  2

• Bug: test suite failure in MACS 3.0.0

  #615 opened 4 months ago by tillea
  18

• Q: conversion of output files to UCSC track hub format?

  #621 opened 5 months ago by maximilianh
  1

• Bug: BEDPE Format input for hmmratac

  #596 opened 5 months ago by bcantarel
  3

• Bug: MACS3 ZeroDivisionError: float division

  #584 opened 5 months ago by bsunbo
  2

• What is the difference between "absolute peak summit" and "summit position" in narrowPeak format?

  #617 opened 5 months ago by mcsimenc
  1

• Bug: pip install error: subprocess-exited-with-error

  #616 opened 5 months ago by ferygood
  2

• Q: question about the libmvec.so.1 error.

  #604 opened 7 months ago by Simple53
  3

• Q: Defining the bin size when generating bedgraphs.

  #614 opened 6 months ago by rikrdo89
  0

• Q: Is there a way to specify blacklisted regions in MACS2?

  #613 opened 6 months ago by rikrdo89
  0

• Bug: HMMRATAC --save-digested outputs four identical signal tracks

  #605 opened 6 months ago by mrendleman
  0

• Mention alternative installation methods in install guide

  #610 opened 6 months ago by outpaddling
  0

• Bug: Test scripts failing

  #609 opened 6 months ago by outpaddling
  1

• Q: lambda estimation

  #608 opened 6 months ago by pegahtak
  0

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

  #607 opened 7 months ago by LoganLHJ
  1

• Q: about the 'max-gap 'parameter

  #603 opened 7 months ago by liuyu988
  0

• Q: the questions about calling broad peaks

  #601 opened 7 months ago by liuyu988
  0

• Use of IDR after running MACS3 for ATAC-seq data

  #599 opened 7 months ago by OrangeyO2
  2

• Bug: python3.12 incompatible due to numpy<1.24 restriction

  #598 opened 8 months ago by jowodo
  7

• Bug:

  #595 opened 10 months ago by XuJahcenia
  1

• Bug: `LINK : fatal error LNK1181: cannot open input file 'm.lib'`

  #594 opened 10 months ago by danli349
  1

• hmmratac adjust means and standard deviation

  #593 opened 10 months ago by LinearParadox
  5

• Bug:

  #591 opened 10 months ago by david2905
  2

• Q: multi sample comparison (scATAC)

  #585 opened a year ago by revolvefire
  0

• Bug: Getting requirements to build wheel ... error

  #583 opened a year ago by bsunbo
  4

• Q: how do slocal amd llocal work with open/closed chromatin domains?

  #582 opened a year ago by linpei26
  0

• Feat: Support to output multiple output formats when using hmmratac mode

  #581 opened a year ago by ketakibhide
  0

• Feat: Support for CRAM

  #578 opened a year ago by bcantarel
  4

• Bug: MACS3 can't installed by pip

  #574 opened a year ago by dengyang111
  2

• Bug: Overly large fragment causes zeroDivision error while calculating weights for four signal tracks.

  #577 opened a year ago by taoliu
  2

• Q: What is recommended command line for ATAC-Seq peak calling with bams from Paired End data

  #571 opened a year ago by tamuanand
  1