Issues
- 2
Downstream analysis tutorial
#319 opened by GaF123 - 2
Annotation of differentially accessible peaks
#299 opened by ayavuzcakir - 3
Vignette for downstream analysis tools?
#315 opened by zrlewis - 1
snap.pp.import_data results in RuntimeError: H5Fcreate(): unable to create file: unable to truncate a file which is already open
#317 opened by wgao688 - 2
How does one import multiple fragments.tsv.gz files from different samples?
#314 opened by yojetsharma - 1
Maintaining Batch Correction in Joint Embedding
#311 opened by meiiemg - 1
The analysis about non-single cell sequencing
#313 opened by allanlinzhang - 1
Extracting fragment count matrix
#316 opened by lf96abc - 1
Can't download pbmc10k_multiome
#309 opened by Li-ZhiD - 0
Unexpected behavior in AnnDataSet subset
#310 opened by mtvector - 0
- 2
snapatac2.tl.diff_test
#306 opened by TingTingShao - 3
- 3
- 3
snap.pp.import_data hangs on 0%
#302 opened by MubasherMohammed - 1
Accessing and plotting QC metrics after merging to AnnDataSet: more documentation needed
#300 opened by jeremymsimon - 0
- 2
Error related to parallelism when running `snap.tl.macs3` when running on the cluster
#298 opened by PauBadiaM - 3
cell number decreased significantly after loading to snapatac as h5ad file
#296 opened by TingTingShao - 0
snap.tl.macs3
#297 opened by TingTingShao - 1
snap.pp.mnc_correct groupby
#292 opened by TingTingShao - 10
AnnData subset function: out cannot be None.
#251 opened by beyondpie - 5
- 1
- 2
make_fragment_file output file is empty
#288 opened by MaoxuWang - 1
AnnDataSet loses the .obsm
#287 opened by wgao688 - 3
make_gene_matrix: cannot set n_obs unless n_obs == 0
#289 opened by wgao688 - 2
add_cor_scores
#286 opened by TingTingShao - 2
Cannot find macs2
#283 opened by RuiyuRayWang - 2
- 5
write anndataset
#258 opened by TingTingShao - 3
save images
#275 opened by TingTingShao - 4
trouble with pbmc notebook
#277 opened by vjcitn - 0
- 5
Read bam with split reads
#259 opened by lauradmartens - 4
import data
#269 opened by TingTingShao - 2
- 0
color by accessibility of a certain region
#270 opened by TingTingShao - 5
AnnDataSet overwritten
#261 opened by TingTingShao - 1
[Question from Beginner] How can I use SnapATAC2 if I don't have BAM file or fragment files?
#265 opened by JiehoonKwak - 0
Integration with SCENICplus
#262 opened by TingTingShao - 1
try different knn methods
#264 opened by TingTingShao - 0
SnapATAC2 Docker Image Pushed to Docker Hub
#263 opened by dtgz-sudo - 1
add_cor_scores could only selects capitalized genes?
#260 opened by zkcao - 5
snakemake workflow
#256 opened by TingTingShao - 1
Analysis of single-cell dataset that includes both single- and paired-end samples?
#250 opened by zhang-jiankun - 4
Too much time for snap.tl.spectral
#252 opened by yuanlizhanshi - 1
- 3
Multi-sample modality pipeline QC
#253 opened by TingTingShao - 3
Installation Failed : M1 Pro, macOS Sonoma 14.3 (cannot install v2.5.3 or v.2.6.0)
#248 opened by JiehoonKwak