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cellranger
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Non-empty droplets versus good quality cells
CellRanger
emptyDrops
scRNAseq
10X
8 months ago
rocanja
▴ 60
0
votes
0
replies
743
views
Read Cellranger outputs in R, combine as SingleCellExperiment
ReadInR
Cellranger
GEX+Features+VDJ
2.8 years ago
gregoire.destreel
• 0
0
votes
1
reply
1.2k
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Aberrant number of cells
CellBarcode
DropletUtils
emptyDrops()
Cellranger
scRNAseq
updated 2.6 years ago by
rohitsatyam102
▴ 20 • written 2.8 years ago by
gregoire.destreel
• 0
7
votes
12
replies
7.8k
views
How to identify real cells in 10X RNA-seq ?
single-cell
10X
Cell calling
DropletUtils
cellranger
updated 5.7 years ago by
Aaron Lun
★ 28k • written 5.7 years ago by
xingxd16
▴ 20
4 results • Page
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Answer: Create Illmina bead summary data
by
Gordon Smyth
51k
GenomeStudio produces IDAT files that you can read using the `read.idat` function in limma. That is the recommended way to read GenomeStudi…
Comment: Help with RSEM counts: do I transpose matrix?
by
NB
• 0
OK thank you.
Comment: Help with RSEM counts: do I transpose matrix?
by
James W. MacDonald
67k
You can ask here, but please read the `DESeq2` vignette first, which should answer most questions.
Comment: Help with RSEM counts: do I transpose matrix?
by
NB
• 0
Thank you. If I have questions about QC/normalization, do I ask them here or ask a new question?
Answer: Help with RSEM counts: do I transpose matrix?
by
James W. MacDonald
67k
Yes. Samples in columns and genes in rows.
Votes
Answer: Detecting genomic signatures of drug resistance breast cancer in transcriptom
Comment: Issues with BSgenome.Mmusculus.UCSC.mm39 and generating motif matrix in Signac (
Answer: Issues with BSgenome.Mmusculus.UCSC.mm39 and generating motif matrix in Signac (
Comment: does anyone how to create rarefaction curves from a phyloseq object?
Answer: ANOVA like approach of edgeR
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