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35 Open 1,236 Closed
35 Open 1,236 Closed
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Issues list

RunChromVAR() fails to find ATAC count data despite the data existing bug Something isn't working
#1914 opened Apr 14, 2025 by vficarrotta
question about initial data processing that were not produced by 10X genomics
#1913 opened Apr 11, 2025 by dahun73
IntegrateEmbeddings: Error in .rowNamesDF<-(x, value = value) : invalid 'row.names' length
#1910 opened Mar 19, 2025 by VilainLab
Scoring peaks accessibility from a list of peaks enhancement New feature or request
#1909 opened Mar 17, 2025 by BERICP01
1
Error: The cell names in the reduction provided don't match the cell names present in the objects used to build the AnchorSet
#1908 opened Mar 13, 2025 by SaharBJ
Internal bug in RegionStats leading to issues with LinkPeaks bug Something isn't working
#1907 opened Mar 12, 2025 by kryptonitecircuit2002
FindMotifs return pvalue with NaN bug Something isn't working
#1905 opened Mar 5, 2025 by nh-codem
Create motif object function and format of positions documentation Documentation help
#1904 opened Feb 27, 2025 by sknaack
LinkPeaks() function not working. Unable to make coverage plots bug Something isn't working
#1902 opened Feb 20, 2025 by zgb963
Support for Large Sparse Matrices in Signac enhancement New feature or request
#1897 opened Feb 6, 2025 by ShanshanHe-44
1
Can you expose CutMatrix and MultiRegionCutMatrix for everyone to use enhancement New feature or request
#1888 opened Jan 18, 2025 by ZhangFuchang
1
Unable to link peaks to genes bug Something isn't working
#1855 opened Nov 26, 2024 by zgb963
10
Unable to subset chromatinassay by features like in vignette "Analyzing PBMC scATAC-seq" when other assays are present bug Something isn't working
#1847 opened Nov 23, 2024 by jzw1999
1
Issues with adding motifs to multiome dataset: Error in loadFUN(x, seqname, ranges) : trying to load regions beyond the boundaries of non-circular sequence "chr1" bug Something isn't working
#1845 opened Nov 22, 2024 by ptk1601
AddMotifs ERROR: Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'xvcopy': some ranges are out of bounds bug Something isn't working
#1815 opened Nov 13, 2024 by elegantmedstu
Suggestion on argument name "max.downsample" in CoveragePlot and related functions
#1791 opened Sep 29, 2024 by G3N0M3
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
2
Integrated scATAC data, dimension set: dims = 2:30 documentation Documentation help
#1783 opened Sep 18, 2024 by YuelinYao
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
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