PMID- 32330223
OWN - NLM
STAT- MEDLINE
DCOM- 20201223
LR  - 20201223
IS  - 1367-4811 (Electronic)
IS  - 1367-4803 (Print)
IS  - 1367-4803 (Linking)
VI  - 36
IP  - 12
DP  - 2020 Jun 1
TI  - scHLAcount: allele-specific HLA expression from single-cell gene expression data.
PG  - 3905-3906
LID - 10.1093/bioinformatics/btaa264 [doi]
AB  - SUMMARY: Bulk RNA sequencing studies have demonstrated that human leukocyte 
      antigen (HLA) genes may be expressed in a cell type-specific and allele-specific 
      fashion. Single-cell gene expression assays have the potential to further resolve 
      these expression patterns, but currently available methods do not perform 
      allele-specific quantification at the molecule level. Here, we present 
      scHLAcount, a post-processing workflow for single-cell RNA-seq data that computes 
      allele-specific molecule counts of the HLA genes based on a personalized 
      reference constructed from the sample's HLA genotypes. AVAILABILITY AND 
      IMPLEMENTATION: scHLAcount is available under the MIT license at 
      https://github.com/10XGenomics/scHLAcount. SUPPLEMENTARY INFORMATION: 
      Supplementary data are available at Bioinformatics online.
CI  - (c) The Author(s) 2020. Published by Oxford University Press.
FAU - Darby, Charlotte A
AU  - Darby CA
AD  - Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, 
      USA.
FAU - Stubbington, Michael J T
AU  - Stubbington MJT
AD  - 10x Genomics, Pleasanton, CA 94588, USA.
FAU - Marks, Patrick J
AU  - Marks PJ
AD  - 10x Genomics, Pleasanton, CA 94588, USA.
FAU - Martinez Barrio, Alvaro
AU  - Martinez Barrio A
AD  - 10x Genomics, Pleasanton, CA 94588, USA.
FAU - Fiddes, Ian T
AU  - Fiddes IT
AD  - 10x Genomics, Pleasanton, CA 94588, USA.
LA  - eng
PT  - Journal Article
PL  - England
TA  - Bioinformatics
JT  - Bioinformatics (Oxford, England)
JID - 9808944
SB  - IM
MH  - Alleles
MH  - Gene Expression
MH  - Humans
MH  - Sequence Analysis, RNA
MH  - *Single-Cell Analysis
MH  - *Software
MH  - Workflow
PMC - PMC7320622
EDAT- 2020/04/25 06:00
MHDA- 2020/12/29 06:00
PMCR- 2020/04/24
CRDT- 2020/04/25 06:00
PHST- 2019/12/06 00:00 [received]
PHST- 2020/04/08 00:00 [revised]
PHST- 2020/04/16 00:00 [accepted]
PHST- 2020/04/25 06:00 [pubmed]
PHST- 2020/12/29 06:00 [medline]
PHST- 2020/04/25 06:00 [entrez]
PHST- 2020/04/24 00:00 [pmc-release]
AID - 5824792 [pii]
AID - btaa264 [pii]
AID - 10.1093/bioinformatics/btaa264 [doi]
PST - ppublish
SO  - Bioinformatics. 2020 Jun 1;36(12):3905-3906. doi: 10.1093/bioinformatics/btaa264.