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shrna
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0
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2
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1.9k
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Using edgeR for small shRNA-seq screen analysis
edger
shrna
8.6 years ago
sirintra
▴ 10
2
votes
2
replies
2.3k
views
Analysis of shRNA screen data
shrna
edger
deseq2
differential expression
normalized counts
9.2 years ago
Jane Merlevede
▴ 90
1
vote
1
reply
1.2k
views
limma for shRNA dropout screen analysis?
limma
gmap
shRNA
dropout screen
updated 9.3 years ago by
Aaron Lun
★ 29k • written 9.3 years ago by
Anna Dvorkin
▴ 40
4
votes
4
replies
2.0k
views
edgeR:processAmplicons barcode match only 57% when it should be 100% -- I artificially inserted them -- are there other assumptions
edgeR
processamplicons
shrna
updated 9.8 years ago by
thomas.leete
• 0 • written 10.0 years ago by
Anne Deslattes Mays
▴ 10
0
votes
5
replies
3.1k
views
example fastq file, sampleAnnotaition and Hairpin file for shRNAseq/EdgeR tool
shRNAseq
edgeR
shRNA
updated 10.0 years ago by
Gordon Smyth
53k • written 10.0 years ago by
KB
▴ 50
5 results • Page
1 of 1
Recent ...
Replies
Comment: JunctionSeq producing strangely large effect sizes for certain exon counting bin
by
97shandie
• 0
That's a tricky issue! I've definitely seen similar behavior in differential exon usage analysis. It sounds like the normalization method J…
Comment: Heat Map
by
97shandie
• 0
Hi Dania, it looks like you're on the right track building your heatmap! It's great you've already filtered your data based on adjusted p-v…
Comment: Help with defining groups
by
Phinney, Brett
▴ 10
I got it working , thank you!!!
Comment: Results with PON give more variants
by
ejafgdf4.ge.r.m
• 0
It s common to expect Mutect2 with a PON to be a strict subset of Mutect2 without it but seeing unique variants in Mutect2withPON isn t unu…
Comment: Check removeBatchEffect effectiveness
by
massimo
• 0
I would kindly ask for additional support. When not including the design_timepoint argument in removeBatchEffect and thus keeping the inter…
Votes
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Comment: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
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