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2
votes
1
reply
794
views
STARsolo sorted bam contains 'non-whitelisted' barcodes
starsolo alignment
updated 9 months ago by ★ 7.7k • written 9 months ago by ▴ 310
0
votes
1
reply
697
views
comparing STARsolo UMI-based directional deduplication vs umi-tools?
single-cell starsolo deduplication umi-tools
updated 9 months ago by 22k • written 9 months ago by ▴ 310
0
votes
1
reply
2.0k
views
Comment: Comment: Understanding STARsolo --soloStrand values and 10X scRNA-seq library structure
9 months ago by mk ▴ 310
5
votes
6
replies
2.0k
views
Understanding STARsolo --soloStrand values and 10X scRNA-seq library structure
10X scRNA-seq stranded
updated 3 months ago by ★ 7.7k • written 9 months ago by ▴ 310
0
votes
0
replies
362
views
why STAR --clip[3p,5p]Nbases show up in the bam?
STAR clipping alignment
updated 10 months ago by 5.1k • written 10 months ago by ▴ 310
0
votes
0
replies
1.3k
views
Comment: Comment: How to include the lane index in STARsolo count matrix barcodes.tsv?
10 months ago by mk ▴ 310
0
votes
1
reply
1.3k
views
Comment: Comment: How to include the lane index in STARsolo count matrix barcodes.tsv?
10 months ago by mk ▴ 310
3
votes
6
replies
1.3k
views
How to include the lane index in STARsolo count matrix barcodes.tsv?
10x starsolo singlecell star alignment
updated 10 months ago by ★ 19k • written 10 months ago by ▴ 310
0
votes
2
replies
821
views
How to perform corrected Cell Barcode/UMI calling with an externally sorted BAM?
bam alignment starsolo star
updated 10 months ago by ★ 7.7k • written 10 months ago by ▴ 310
0
votes
1
reply
989
views
Comment: Comment: Where does cellranger log its estimates for the input to DETECT_COUNT_CHEMISTRY?
15 months ago by mk ▴ 310
0
votes
3
replies
989
views
Where does cellranger log its estimates for the input to DETECT_COUNT_CHEMISTRY?
cellranger sequencing single-cell
updated 15 months ago by 89k • written 15 months ago by ▴ 310
0
votes
2
replies
1.5k
views
how to get sequences by location when pyfaidx.Fasta(read_long_names=True) creates keys from FastaRecord (dmel r6 genome build)?
selene_sdk pyfaidx fasta python flybase
updated 21 months ago by ★ 2.1k • written 21 months ago by ▴ 310
0
votes
0
replies
1.5k
views
Answer: Answer: how to get sequences by location when pyfaidx.Fasta(read_long_names=True) create
21 months ago by mk ▴ 310
0
votes
0
replies
1.2k
views
use GEOparse to download series supplemental files?
gse geoparse python geoquery geo
21 months ago by mk ▴ 310
3
votes
2
replies
1.3k
views
use bioservices.UniProt (python) to map uniprot accession to [multiple] ensembl ids
bioservices ensembl python uniprot
22 months ago by mk ▴ 310
2
votes
0
replies
1.3k
views
Answer: Answer: use bioservices.UniProt (python) to map uniprot accession to [multiple] ensembl
22 months ago by mk ▴ 310
2
votes
0
replies
4.8k
views
Answer: Answer: GeneActivity without Fragments file in Seurat for Integrating scRNA-seq and scAT
2.5 years ago by mk ▴ 310
0
votes
0
replies
510
views
pathwaycommons SPARQL endpoint down?
pathway-commons
updated 2.3 years ago by 45k • written 2.7 years ago by ▴ 310
0
votes
1
reply
897
views
Any way to search [GEO, etc] by library prep protocol (looking for published single-cell multi-ome data)?
single-cell atac-seq rna-seq multiomics
updated 2.9 years ago by 154k • written 2.9 years ago by ▴ 310
0
votes
0
replies
921
views
Comment: Comment: does bioconductor/bioconductor_docker:RELEASE_X_Y install CRAN packages from a f
3.6 years ago by mk ▴ 310
2
votes
2
replies
921
views
does bioconductor/bioconductor_docker:RELEASE_X_Y install CRAN packages from a fixed snapshot?
R Bioconductor docker
3.6 years ago by mk ▴ 310
0
votes
1
reply
6.5k
views
Comment: Comment: seurat `<obj>@assays$RNA@counts` vs `<obj>@assays$RNA@data`?
4.1 years ago by mk ▴ 310
0
votes
0
replies
5.0k
views
Comment: Comment: how to Seurat::RunUMAP() but run reduction="pca" on subset of features?
4.1 years ago by mk ▴ 310
0
votes
0
replies
5.0k
views
Comment: Comment: how to Seurat::RunUMAP() but run reduction="pca" on subset of features?
4.1 years ago by mk ▴ 310
1
vote
4
replies
5.0k
views
how to Seurat::RunUMAP() but run reduction="pca" on subset of features?
seurat pca umap
4.1 years ago by mk ▴ 310
0
votes
1
reply
6.5k
views
Comment: Comment: seurat `<obj>@assays$RNA@counts` vs `<obj>@assays$RNA@data`?
4.1 years ago by mk ▴ 310
1
vote
5
replies
6.5k
views
seurat `<obj>@assays$RNA@counts` vs `<obj>@assays$RNA@data`?
seurat
updated 4.1 years ago by 13k • written 4.1 years ago by ▴ 310
1
vote
0
replies
2.2k
views
Comment: Comment: AnnotationHub::mapIds() cannot find existing ENSG (GEO supplemental data cross-r
4.1 years ago by mk ▴ 310
1
vote
0
replies
2.2k
views
Comment: Comment: AnnotationHub::mapIds() cannot find existing ENSG (GEO supplemental data cross-r
4.1 years ago by mk ▴ 310
5
votes
3
replies
2.2k
views
AnnotationHub::mapIds() cannot find existing ENSG (GEO supplemental data cross-referenced with ensembl.org)
ensg annotationhub mapping
4.1 years ago by mk ▴ 310
0
votes
0
replies
1.2k
views
where to get PBMC (68k) labels?
pbmc single-cell 10x
4.6 years ago by mk ▴ 310
0
votes
0
replies
883
views
database of ligand->receptor->TF(or transcriptional target)
database signaling
updated 4.9 years ago by 20 • written 5.0 years ago by ▴ 310
0
votes
0
replies
1.2k
views
Published data sets using 10x Feature Barcoding?
10x single-cell 10x genomics feature barcoding
4.9 years ago by mk ▴ 310
1
vote
0
replies
4.7k
views
Comment: C: what is the deal with bioconda?
4.9 years ago by mk ▴ 310
8
votes
4
replies
4.7k
views
what is the deal with bioconda?
conda bioconda
updated 4.4 years ago by ▴ 140 • written 4.9 years ago by ▴ 310
0
votes
0
replies
1.5k
views
Comment: C: content negotiation for the ontobee sparql endpoint
updated 5.0 years ago by 45k • written 5.0 years ago by ▴ 310
0
votes
2
replies
1.5k
views
Comment: C: content negotiation for the ontobee sparql endpoint
5.0 years ago by mk ▴ 310
1
vote
1
reply
1.5k
views
Comment: C: content negotiation for the ontobee sparql endpoint
5.0 years ago by mk ▴ 310
4
votes
6
replies
1.5k
views
content negotiation for the ontobee sparql endpoint
ontobee sparql obofoundry
5.0 years ago by mk ▴ 310
3
votes
2
replies
1.5k
views
error when trying to perform a federated query in Pathway Commons SPARQL endpoint
uniprot pathway-commons rdf sparql biopax
updated 2.3 years ago by 45k • written 5.0 years ago by ▴ 310
0
votes
0
replies
1.6k
views
Comment: C: what is the uniprot RDF entity for "uniprot accession"?
5.0 years ago by mk ▴ 310
3
votes
2
replies
1.6k
views
what is the uniprot RDF entity for "uniprot accession"?
uniprot rdf
updated 5.0 years ago by ▴ 760 • written 5.0 years ago by ▴ 310
1
vote
2
replies
4.6k
views
Creation of cellDataSet in Monocle 2 wants undocumented AnnotatedDataFrame: assayData
monocle cellDataSet ExpressionSet
updated 5.0 years ago by • 0 • written 7.7 years ago by ▴ 310
1
vote
0
replies
1.3k
views
Answer: A: Are federated SPARQL queries pointless with the Pathway Commons BioPAX represent
5.0 years ago by mk ▴ 310
1
vote
1
reply
1.3k
views
Are federated SPARQL queries pointless with the Pathway Commons BioPAX representation?
ontology BioPAX SPARQL wikipathways reactome
5.0 years ago by mk ▴ 310
0
votes
0
replies
1.3k
views
Comment: C: censoring time for ICGC records with no followup or date of death?
5.2 years ago by mk ▴ 310
1
vote
2
replies
1.3k
views
censoring time for ICGC records with no followup or date of death?
icgc survival cancer
5.3 years ago by mk ▴ 310
1
vote
0
replies
1.3k
views
Comment: C: ICGC mRNA sequencing data: where is the documentation on analysis_id?
5.3 years ago by mk ▴ 310
0
votes
0
replies
1.4k
views
Comment: C: Entrez e-utils reference for ensembl ids
5.3 years ago by mk ▴ 310
2
votes
4
replies
1.3k
views
ICGC mRNA sequencing data: where is the documentation on analysis_id?
icgc RNA-Seq
5.3 years ago by mk ▴ 310
76 results • Page 1 of 2
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