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238 Open 303 Closed
238 Open 303 Closed
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Issues list

Q: the likelihood of bdgdiff General Question
#681 opened Dec 13, 2024 by BenxiaHu
Bug: No peaks detected in not-blacklisted regions when a blacklist is given to macs3 hmmratac Bug Report
#680 opened Dec 5, 2024 by MariaRig
Q: Haplotype genomes have no peak General Question
#679 opened Dec 4, 2024 by bigshark12345
Q: AssertionError: No proper d can be found! Tweak --mfold? General Question
#677 opened Nov 22, 2024 by nanu23333
About ATAC-seq call peak (hmmratac) and differential analysis via MACS3
#676 opened Nov 19, 2024 by DayTimeMouse
Q: There's a huge difference between my peak number and the bio company's peak number General Question
#673 opened Nov 14, 2024 by bigshark12345
2
Bug: NameError: name 'BedGraphIO' is not defined. Did you mean: 'bedGraphIO'? Bug Report
#672 opened Nov 13, 2024 by acv21
1
Q: MACS3 hmmratac for single-cell ATAC-seq General Question
#671 opened Nov 11, 2024 by acv21
Q: gappedPeak instead of narrow peak on HMMRATAC output General Question
#670 opened Oct 29, 2024 by jffpviana
3
Q: Filtering blacklisted regions when using macs3 hmmeratac General Question
#669 opened Oct 24, 2024 by eggrandio
1
Bug: Overflow error when using Poisson law for bdgcmp Bug Report
#667 opened Oct 22, 2024 by callum-b
3
Bug: Runtime error pybind11::handle::inc_ref() PyGILState_Check() failure. Bug Report
#666 opened Oct 21, 2024 by Kiliankleemann
@taoliu
1
Feat: Multiprocessing for calling peaks (1 process per chromosome) Feature Request
#665 opened Oct 9, 2024 by jeanmonet
Bug: Illegal instruction (core dumped) Bug Report
#663 opened Oct 7, 2024 by marinafloresp
@taoliu
1
Q: What parameters should I need to tweak for viral ChipSeq General Question
#656 opened Sep 2, 2024 by Rohit-Satyam
1
Better cutoff levels control for bdgcallpeak cutoff-analysis Feature Request
#654 opened Jul 22, 2024 by callum-b
1
Q: using macs3 to detect peaks on long-read readings General Question
#652 opened Jul 2, 2024 by MJoseMo
Feat: Add --call-summits option in MACS3 bdgpeakcall? Feature Request
#651 opened Jun 26, 2024 by alicewang19
Number of de-duplicated reads indicated by filterdup log does not match number of lines in output BED file. Bug Report
#650 opened Jun 20, 2024 by callum-b
Bug: OverflowError when running hmmratac Bug Report
#649 opened Jun 19, 2024 by atj31
Q: How to use HMMRATAC to give us a narrow peak file and have signalValue, p and q-value ? General Question
#648 opened Jun 13, 2024 by MinaMyr
1
Setting cut-off when using logFE bigWig files from bdgcmp General Question
#646 opened May 29, 2024 by manjumoorthy95
Bug: Callvar throws an error when run on broadPeak file Bug Report
#643 opened May 2, 2024 by LinearParadox
@taoliu
15
Q: how to use MACS3 for ATAC seq with "himmratac" option? General Question
#639 opened Apr 20, 2024 by kbarrr
2
Q: HMMRATAC reproducibility General Question
#638 opened Apr 4, 2024 by igordot
2
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