kaizhang SnapATAC2 issues

kaizhang / SnapATAC2

Single-cell epigenomics analysis tools

https://kzhang.org/SnapATAC2/

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issues

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The analysis about non-single cell sequencing

#313 allanlinzhang opened 6 days ago
0
Maintaining Batch Correction in Joint Embedding

#311 meiiemg opened 1 week ago
0
Unexpected behavior in AnnDataSet subset

#310 mtvector opened 2 weeks ago
0
Can't download pbmc10k_multiome

#309 Li-ZhiD closed 6 days ago
1
Specify that all features are used if sample_size is None

#307 newtonharry opened 1 month ago
0
snapatac2.tl.diff_test

#306 TingTingShao opened 1 month ago
2
`TypeError: fork_exec() takes exactly 23 arguments (17 given)`

#305 nleroy917 closed 1 month ago
3
How to calculate TSS(UP 1K,DOWN 1K) score for gene of every cell?

#304 mengchengyao closed 1 month ago
3
snap.pp.import_data hangs on 0%

#302 MubasherMohammed closed 2 months ago
3
Bug: barcode_regex="(..:..:..:..):w+$" shown in the document

#301 beyondpie closed 2 months ago
0
Accessing and plotting QC metrics after merging to AnnDataSet: more documentation needed

#300 jeremymsimon opened 2 months ago
1
Annotation of differentially accessible peaks

#299 ayavuzcakir closed 1 month ago
1
Error related to parallelism when running `snap.tl.macs3` when running on the cluster

#298 PauBadiaM opened 2 months ago
2
snap.tl.macs3

#297 TingTingShao opened 2 months ago
0
cell number decreased significantly after loading to snapatac as h5ad file

#296 TingTingShao closed 2 months ago
3
snap.pp.mnc_correct groupby

#292 TingTingShao closed 2 months ago
1
lots of integers in the python REPL during running spectral embedding

#291 beyondpie closed 3 months ago
5
hard to understand about the description in filter features.

#290 beyondpie opened 3 months ago
1
make_gene_matrix: cannot set n_obs unless n_obs == 0

#289 wgao688 closed 3 months ago
3
make_fragment_file output file is empty

#288 MaoxuWang closed 3 months ago
2
AnnDataSet loses the .obsm

#287 wgao688 closed 3 months ago
1
add_cor_scores

#286 TingTingShao opened 3 months ago
2
Fix CI errors

#284 njmei closed 1 month ago
0
Cannot find macs2

#283 RuiyuRayWang closed 3 months ago
2
Fix failing docker image builds

#282 njmei closed 3 months ago
2
Fix notebook bugs and dependency issues

#281 njmei closed 3 months ago
2
obs_names resets to original barcodes when assigned via AnnDataset

#278 newtonharry opened 3 months ago
0
trouble with pbmc notebook

#277 vjcitn opened 3 months ago
4
scanpy AnnData to snapatac2 AnnData: cannot read csr_matrix

#276 beyondpie opened 3 months ago
2
save images

#275 TingTingShao closed 3 months ago
3
info lost after converting anndataset into anndata

#271 TingTingShao closed 3 months ago
2
color by accessibility of a certain region

#270 TingTingShao opened 3 months ago
0
import data

#269 TingTingShao closed 3 months ago
4
[Question from Beginner] How can I use SnapATAC2 if I don't have BAM file or fragment files?

#265 JiehoonKwak closed 3 months ago
1
try different knn methods

#264 TingTingShao closed 3 months ago
1
SnapATAC2 Docker Image Pushed to Docker Hub

#263 dtgz-sudo opened 3 months ago
0
Integration with SCENICplus

#262 TingTingShao closed 3 months ago
0
AnnDataSet overwritten

#261 TingTingShao closed 3 months ago
5
add_cor_scores could only selects capitalized genes?

#260 zkcao opened 3 months ago
1
Read bam with split reads

#259 lauradmartens opened 3 months ago
5
write anndataset

#258 TingTingShao closed 3 months ago
5
snakemake workflow

#256 TingTingShao closed 3 months ago
5
import_data() got multiple values for argument 'chrom_sizes'

#255 TingTingShao closed 3 months ago
1
Multi-sample modality pipeline QC

#253 TingTingShao closed 3 months ago
3
Too much time for snap.tl.spectral

#252 yuanlizhanshi closed 3 months ago
4
AnnData subset function: out cannot be None.

#251 beyondpie closed 3 months ago
10
Analysis of single-cell dataset that includes both single- and paired-end samples?

#250 zhang-jiankun closed 3 months ago
1
Improve Docker images usability

#249 njmei closed 3 months ago
1
Installation Failed : M1 Pro, macOS Sonoma 14.3 (cannot install v2.5.3 or v.2.6.0)

#248 JiehoonKwak closed 4 months ago
3
snap.pp.import_data with list of fragment files and list of files containing whitelist barcodes

#247 strohstern opened 4 months ago
2