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30 Open 1,186 Closed
30 Open 1,186 Closed
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Issues list

I'm running a scATAC-seq analysis. However, the peaks I've called are somehow weird bug Something isn't working
#1804 opened Oct 17, 2024 by TideJunior
integration of several multiome datasets documentation Documentation help
#1801 opened Oct 10, 2024 by mengm5
When installing it on a new system bug Something isn't working
#1800 opened Oct 9, 2024 by stela2502
1
Reproducing CoveragePlot results during differential peak analysis documentation Documentation help
#1795 opened Oct 4, 2024 by si3
Use Signac with annotation from gtf file documentation Documentation help
#1793 opened Sep 30, 2024 by lldelisle
2
Suggestion on argument name "max.downsample" in CoveragePlot and related functions
#1791 opened Sep 29, 2024 by G3N0M3
How sequencing depth impacts the number of DARs? documentation Documentation help
#1789 opened Sep 27, 2024 by sshanyiiii
Error in Motif Analysis bug Something isn't working
#1788 opened Sep 26, 2024 by yangxinzhi
Metagene plots enhancement New feature or request
#1787 opened Sep 25, 2024 by diego-rt
Following integration of multiple samples, SVD producing all NA cell embeddings bug Something isn't working
#1786 opened Sep 25, 2024 by gherrgo
1
Integrated scATAC data, dimension set: dims = 2:30 documentation Documentation help
#1783 opened Sep 18, 2024 by YuelinYao
Coverageplot freezes R bug Something isn't working
#1781 opened Sep 13, 2024 by AnaisJulien
Error in collect() Aug 20 Analyzing PBMC scATAC-seq tutorial bug Something isn't working
#1780 opened Sep 10, 2024 by SaharBJ
1
RegionHeatmap order
#1745 opened Jul 10, 2024 by umutcakir
10X multiome subsetting cancer cell line with blacklist_ratio ~ 1 for both hg38_blacklist and hg38_blacklist_unified
#1741 opened Jul 9, 2024 by methornton
4
Options for ncol and keeping order of idents in RegionHeatmap enhancement New feature or request
#1729 opened Jun 21, 2024 by mossconfuse
Footprinting issue bug Something isn't working
#1689 opened Apr 23, 2024 by leecon30
1
Check for MACS2 before splitting file enhancement New feature or request
#1678 opened Apr 5, 2024 by AmelZulji
3
TSS enrichment with a region extension 2000bp
#1638 opened Feb 26, 2024 by Montsecb
4
Solution for errors related to as_cholmod_sparse or CRsparse_rowSums
#1596 opened Jan 18, 2024 by timoast
8
BPcells doesn't work with chromatin Assay enhancement New feature or request
#1507 opened Oct 10, 2023 by LucaTucciarone
4
ReadMGATK does not work if using -eb option in mgatk bug Something isn't working
#1462 opened Jul 31, 2023 by msteph11
1
Changing Fragment object annotation style enhancement New feature or request
#1370 opened Apr 4, 2023 by daccachejoe
1
FeatureMatrix() should count cut sites? enhancement New feature or request
#1369 opened Apr 4, 2023 by nesetozel
2
Error adding gene names to the differentially accessible peaks enhancement New feature or request
#1337 opened Feb 14, 2023 by KshitijDeoghar
2
ProTip! Adding no:label will show everything without a label.