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stuart-lab
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signac
R toolkit for the analysis of single-cell chromatin data
https://stuartlab.org/signac/
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How can I remove the ident names from the coverage plot?
#1734
GuiSeSanz
closed
10 hours ago
3
convert signac object to archR
#1733
Byronxy
closed
3 days ago
1
Question for interpreting motif analysis result
#1732
dbswls0322
closed
3 days ago
1
Multiome object on new machine, CoveragePlot Error: TabixFile: Fragment file is not indexed
#1730
NathanKochhar
closed
1 week ago
1
Options for ncol and keeping order of idents in RegionHeatmap
#1729
mossconfuse
opened
1 week ago
0
When batch correction cannot be effectively performed, how should it be handled?
#1727
Dragonlongzhilin
closed
1 week ago
0
gene not found in biotypes for GeneActivities()
#1726
cristanchoa
closed
1 week ago
2
CoveragePlot function: Unable to subset cells
#1724
wenweixiong
closed
1 week ago
1
differential test for atacseq data alone
#1721
dedeepyavaka
closed
2 weeks ago
0
Unable to download pbmc_multimodal.h5seurat object
#1720
Urja25
closed
2 weeks ago
0
LinkPeaks Error in .width_as_unnamed_integer
#1717
JHCCoder
closed
3 weeks ago
4
Integration scATAC with scRNAseq not multiomic
#1715
yamihn
closed
2 weeks ago
0
CreatefragmentObject empty
#1714
yamihn
closed
1 month ago
2
Warning: Error in InsertionBias.ChromatinAssay: Not all hexamers represented in input region
#1713
luoyyyy
opened
1 month ago
8
Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds when running FindIntegrationAnchors
#1712
sropri92
opened
1 month ago
10
The normalized signal is zero in CoveragePlot after subset
#1711
ZhengJIN94
closed
2 weeks ago
2
Only show Links associated with promoter
#1710
KunFang93
closed
1 month ago
1
Error: Cannot find 'ATAC' in this Seurat object
#1709
KunFang93
closed
1 month ago
1
Generate .tbi file from fragments.tsv.gz
#1708
wz0527
closed
1 month ago
1
Error with seqlevelsStyle(annotations) <- "UCSC" command
#1707
sandrews02
closed
1 month ago
1
LinkPeaks, FindMarkers functions not working on RStudio AWS Server
#1706
chsnys
opened
1 month ago
1
Integrating multiple objects with IntegrateEmbeddings() erases all previous reductions
#1705
hannanw
closed
1 month ago
1
result <- ImmuCellAI_new( expr_data_log2, microarray,1,1) Error in `rownames<-`(`*tmp*`, value = colnames(countData)) : attempt to set 'rownames' on an object with no dimensions Called from: `rownames<-`(`*tmp*`, value = colnames(countData))
#1704
elbakrifz
closed
1 month ago
1
seqlengths(NTs.atac.seu) return NULL
#1703
KunFang93
closed
1 month ago
2
FeatureMatrix On Merged Object Returning Empty Matrix
#1701
westonelison
closed
1 month ago
1
Fix track heigh to specific value [`CoveragePlot`]
#1700
jgarces02
closed
1 month ago
0
rror in LinkPeaks
#1698
shabs24
closed
1 month ago
2
When opening an RDS file only in one computer: Error: TabixFile: Fragment file is not indexed.
#1696
nelmari
closed
1 month ago
2
Error encountered by the Coverageplot function
#1694
wxpbioinfo
closed
2 months ago
0
I am getting an error when I use RunTFIDF
#1693
TsviyaOlender
closed
1 month ago
2
TSS enrichment is different in cellranger report and Signac
#1691
Shuresearcher
closed
1 month ago
1
About merging objects
#1690
CCGOGO12
closed
1 month ago
0
Footprinting issue
#1689
leecon30
opened
2 months ago
1
Question about nucleosome signal NA values
#1688
danielcgingerich
closed
2 months ago
3
Question about detecting pseudobulk DACRs with FindMarkers() using DESeq2
#1686
yls2g13
closed
2 months ago
1
Error in TSSEnrichment with Seurat V5 object
#1683
danielcgingerich
closed
2 months ago
1
Error in ClosestFeature function
#1681
emanuelavilla
closed
2 months ago
3
AddChromatinModule function creates NA values in some cells
#1680
Ryuichi30
closed
2 weeks ago
1
LinkPeaks Error: argument 'x' must be numeric
#1679
rishikadaswani
closed
2 months ago
2
Check for MACS2 before splitting file
#1678
AmelZulji
opened
2 months ago
3
Error when merge scATAC data from a list
#1676
Yijia-Jiang
closed
2 months ago
3
regionmatrix very slow
#1675
yamihn
closed
2 months ago
1
Error with install signac
#1670
emanuelavilla
closed
3 months ago
1
how to compare across samples, is it already possible?
#1668
BartBryant
closed
3 months ago
1
RunChromVAR issue when selecting backgroud regions
#1667
FFeiKong
closed
2 months ago
2
FindMotifs( ) error, 'Error in density.default(x=query.feature[[featmatch]], kernel=......'
#1666
BartBryant
closed
3 months ago
3
"CRsparse_rowSums" not resolved from current namespace (Matrix), error with FindMarkers
#1665
BartBryant
closed
3 months ago
1
issue with 'CreateSeuratObject( ),'error in counts$'Gene Expression'
#1664
BartBryant
closed
3 months ago
2
scRNAseq data import without .h5 file
#1663
BartBryant
closed
3 months ago
1
Error: is(object = cds, class2 = "CellDataSet") is not TRUE
#1661
Raghav1881
closed
3 months ago
1
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