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shRNA
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0
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2
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Using edgeR for small shRNA-seq screen analysis
edger
shrna
7.8 years ago
sirintra
▴ 10
2
votes
2
replies
2.1k
views
Analysis of shRNA screen data
shrna
edger
deseq2
differential expression
normalized counts
8.4 years ago
Jane Merlevede
▴ 90
1
vote
1
reply
1.1k
views
limma for shRNA dropout screen analysis?
limma
gmap
shRNA
dropout screen
updated 8.5 years ago by
Aaron Lun
★ 28k • written 8.5 years ago by
Anna Dvorkin
▴ 40
4
votes
4
replies
1.8k
views
edgeR:processAmplicons barcode match only 57% when it should be 100% -- I artificially inserted them -- are there other assumptions
edgeR
processamplicons
shrna
updated 9.0 years ago by
thomas.leete
• 0 • written 9.2 years ago by
Anne Deslattes Mays
▴ 10
0
votes
5
replies
2.9k
views
example fastq file, sampleAnnotaition and Hairpin file for shRNAseq/EdgeR tool
shRNAseq
edgeR
shRNA
updated 9.2 years ago by
Gordon Smyth
52k • written 9.2 years ago by
KB
▴ 50
5 results • Page
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Comment: lfcShrink and alpha value
by
cropero
• 0
Thank you so much! Would that be equivalent to perform `res <- results(dds, contrast = c("conditions", "wild_type_114_2_no_carbon", "wild_t…
Comment: pathview - multiple states
by
Philippine
• 0
Thank you! Here a subset of genes that really works with "ame04145". data <- data.frame( EntrezID = c(100577548, 100577764, 406…
Comment: pathview - multiple states
by
Guido Hooiveld
★ 4.1k
A quick comment after I copied/pasted your code: when using `geneList1` in the 3rd code chunk I do **not** get a nice plot... I rather got …
Answer: scuttle::perFeatureQCMetrics runs very slow for big scRNA-seq data
by
Adam
• 0
Hi Aaron, Thanks a lot for your help! As you mentioned, I checked my data and it is "DelayedMatrix". I don't know the detailed differe…
Answer: scuttle::perFeatureQCMetrics runs very slow for big scRNA-seq data
by
Aaron Lun
★ 28k
You don't mention how your matrix data is being represented, but if it's a file-backed matrix (e.g., `HDF5Matrix` or one of its variants, b…
Votes
Answer: contrast matrix design for a continuous variable
A: What's the difference between p.adjust and qvalue?
Answer: DESeq2- merging technical vs biological replicates
Comment: What type of counts data to import for performing Isoform analysis in edgeR
Answer: What type of counts data to import for performing Isoform analysis in edgeR
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