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shrna
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2
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1.7k
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Using edgeR for small shRNA-seq screen analysis
edger
shrna
7.7 years ago
sirintra
▴ 10
2
votes
2
replies
2.0k
views
Analysis of shRNA screen data
shrna
edger
deseq2
differential expression
normalized counts
8.3 years ago
Jane Merlevede
▴ 90
1
vote
1
reply
1.1k
views
limma for shRNA dropout screen analysis?
limma
gmap
shRNA
dropout screen
updated 8.4 years ago by
Aaron Lun
★ 28k • written 8.4 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 8.9 years ago by
thomas.leete
• 0 • written 9.1 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 9.1 years ago by
Gordon Smyth
51k • written 9.1 years ago by
KB
▴ 50
5 results • Page
1 of 1
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Comment: Consistent Decimals In Data After Antibody Array Background Correction Using Lim
by
Ai
• 0
Hi Gordon, Thank you so much for answering my question and confirming that this is expected! I will go ahead note this down. Sincerely, …
Answer: Annotation for EPICv2
by
icecreamlover
• 0
Hello, I am also working on analyzing my data from EPICv2 using ChAMP. I used this resource as a guide: https://github.com/YuanTian1991/ChA…
Comment: Combining RNAseq and microarray data using edgeR/limma-voom
by
James W. MacDonald
67k
And it doesn't matter if you're doing gene set analyses after, if the statistics are questionable to begin with.
Comment: Combining RNAseq and microarray data using edgeR/limma-voom
by
James W. MacDonald
67k
If you're saying that (as an example) you have treated and control in both assay types, and you want to combine and make comparisons betwee…
Comment: incomplete official symbol mitochondrial genes in org.Hs.eg.db?
by
Guido Hooiveld
★ 4.1k
I have contacted NCBI, and meanwhile got an an answer. See below. It turns out that the official, HGNC-approved symbols are present in the…
Votes
Answer: Consistent Decimals In Data After Antibody Array Background Correction Using Lim
A: How does edgeR cpm function calculate log(CPM) values?
Answer: DecideTest vs topTAGs in edgeR
Comment: DESeq Input from Salmon + tximport/tximeta
Comment: DESeq Input from Salmon + tximport/tximeta
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