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Issues list

Q: HMMRATAC cutoff analysis need help with choosing cutoffs General Question
#701 opened May 8, 2025 by budeer
Q: There is a problem when I use macs3 bdgpeakcall General Question
#700 opened Apr 28, 2025 by GivingupCoke
Bug: cannot install MACS3 by conda Bug Report
#699 opened Apr 12, 2025 by Bencshan
3
Bug: Bug Report
#698 opened Apr 7, 2025 by bbimber
hmmratac: ValueError: Adjust --means and --stddev options and re-run command Bug Report
#697 opened Apr 7, 2025 by bbimber
1
Q: split chromosomes General Question
#696 opened Apr 4, 2025 by zhengluo-zz
1
Bug: pileup with -f FRAG yields OverflowError Bug Report
#695 opened Mar 25, 2025 by jacob-greene
@taoliu
2
Documentation: Missing test files and errors when running commands from tutorial General Question
#693 opened Feb 27, 2025 by bentyeh
1
Q: How many fragments are generally sufficient for hmmratac function? General Question
#687 opened Feb 12, 2025 by leqi0001
3
Q: ERROR: Could not build wheels for cykhash, which is required to install pyproject.toml-based projects General Question
#684 opened Feb 3, 2025 by Eunbi9561
3
Q: the likelihood of bdgdiff General Question
#681 opened Dec 13, 2024 by BenxiaHu
3
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
@taoliu
2
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
3
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
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