stuart-lab signac issues

stuart-lab / signac

R toolkit for the analysis of single-cell chromatin data

https://stuartlab.org/signac/

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issues

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Unable to subset chromatinassay by features like in vignette "Analyzing PBMC scATAC-seq" when other assays are present

#1847 jzw1999 opened 1 day ago
1
FindTransferAnchors error !!

#1846 synatkeamsk opened 1 day ago
0
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"

#1845 ptk1601 opened 1 day ago
0
Dstyaaaaaa patch 1

#1818 dstyaaaaaa closed 2 days ago
0
custom path for fragment files

#1817 Jingyi-Wu-lab closed 3 days ago
1
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

#1815 elegantmedstu opened 1 week ago
0
Assertion `compressBound(0xff00) < 0x10000' failed when using Sinac

#1814 Caewo closed 1 week ago
3
What does this error mean and how can I fi x it in R studio on a mac?

#1812 zunny-d closed 2 weeks ago
0
Coverage Plot: Move axis and gene annotations above tracks

#1811 harrsha4 closed 2 weeks ago
1
Failed to install signac. Error: object ‘recvData’ is not exported by 'namespace:parallel'

#1809 elegantmedstu closed 4 weeks ago
1
Motif footprinting for my data

#1808 dp-sun opened 1 month ago
1
The 'Call peaks' program sets all peak lengths to 501bp.

#1807 ZengMuo closed 1 week ago
1
No Cluster ID's present when making UMAP for Joint RNA and ATAC analysis: 10x multiomic tutorial

#1806 zgb963 closed 1 month ago
2
Error in LinkPeaks: Deprecated Sparse Matrix Conversion ('dgTMatrix') in Matrix Package

#1805 ahdee closed 1 month ago
1
I'm running a scATAC-seq analysis. However, the peaks I've called are somehow weird

#1804 TideJunior closed 1 month ago
1
Better control the number of GRanges

#1803 lldelisle opened 1 month ago
0
fix cases when regions are absent from motif.matrix

#1802 lldelisle opened 1 month ago
1
integration of several multiome datasets

#1801 mengm5 opened 1 month ago
0
When installing it on a new system

#1800 stela2502 closed 1 month ago
1
Freezing/Crashing in RStudio when reading in Multiomics data

#1798 zgb963 closed 1 month ago
2
Be more flexible for annotation

#1797 lldelisle closed 1 month ago
2
Error in CreateChromatinAssay

#1796 Geogres closed 1 month ago
1
Reproducing CoveragePlot results during differential peak analysis

#1795 si3 opened 1 month ago
0
Use Signac with annotation from gtf file

#1793 lldelisle opened 1 month ago
2
Suggestion on argument name "max.downsample" in CoveragePlot and related functions

#1791 G3N0M3 opened 1 month ago
0
subset Fragment file after filtering cells

#1790 sshanyiiii closed 1 month ago
1
How sequencing depth impacts the number of DARs?

#1789 sshanyiiii opened 1 month ago
0
Error in Motif Analysis

#1788 yangxinzhi closed 1 month ago
1
Metagene plots

#1787 diego-rt opened 1 month ago
0
Following integration of multiple samples, SVD producing all NA cell embeddings

#1786 gherrgo opened 1 month ago
1
Cannot add ATAC assay to Seurat Object? Following "Joint RNA and ATAC analysis: 10x multiomic" Vignette

#1785 sohkhar closed 1 month ago
0
Integrated scATAC data, dimension set: dims = 2:30

#1783 YuelinYao opened 2 months ago
0
Coverageplot freezes R

#1781 AnaisJulien closed 1 week ago
2
Error in `collect()` Aug 20 Analyzing PBMC scATAC-seq tutorial

#1780 SaharBJ closed 1 month ago
2
Issue Integrating two 10x multimodal datasets

#1779 sky5198 closed 2 months ago
1
Error in LinkPeaks

#1778 NNnadi closed 2 months ago
1
Recommendation to regress out confounding variables in scatac dataset?

#1776 ejc043 closed 2 months ago
0
CoveragePlot formatting

#1775 jenellewallace closed 2 months ago
1
Error in ConvertMotifID.Assay(object = object[[assay]], ...) : Cannot run ConvertMotifID on a standard Assay object

#1773 Ahmed-Ghobashi closed 3 months ago
1
Unable to find 'nCount_peaks' in Signac data

#1772 ptk1601 closed 3 months ago
2
`CoveragePlot` Error in `colnames<-`(`*tmp*`, value = start(x = region):end(x = region)) : attempt to set 'colnames' on an object with less than two dimensions

#1770 danli349 closed 3 months ago
3
CreateMotifObject error

#1769 sugiYag closed 3 months ago
1
`CreateMotifMatrix` Error in fixupDN.if.valid(value, x@Dim) : length of Dimnames[[1]] (1) is not equal to Dim[1] (0)

#1768 danli349 closed 3 months ago
5
FindTransferAnchors replacement error

#1767 fahmadimoughari closed 3 months ago
1
Seqinfo object

#1765 Guliariel closed 3 months ago
1
how to do monocle3 by standard 10x output files

#1764 GaF123 closed 3 months ago
1
**Error in slice_sample(): ! n must be a round number, not the number 1146.4.

#1763 GaF123 closed 3 months ago
10
SNP infomation

#1761 nhu-github closed 3 months ago
0
Significant Discrepancy in Peak Counts Between Cell Ranger ATAC and Signac Peak Calling

#1760 mano2991 closed 3 months ago
1
An error about "RunChromVAR"

#1758 ZengMuo closed 3 months ago
2