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shRNA
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0
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2
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1.5k
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Using edgeR for small shRNA-seq screen analysis
edger
shrna
7.2 years ago
sirintra
▴ 10
2
votes
2
replies
1.9k
views
Analysis of shRNA screen data
shrna
edger
deseq2
differential expression
normalized counts
7.8 years ago
Jane Merlevede
▴ 90
1
vote
1
reply
979
views
limma for shRNA dropout screen analysis?
limma
gmap
shRNA
dropout screen
updated 7.9 years ago by
Aaron Lun
★ 28k • written 7.9 years ago by
Anna Dvorkin
▴ 40
4
votes
4
replies
1.6k
views
edgeR:processAmplicons barcode match only 57% when it should be 100% -- I artificially inserted them -- are there other assumptions
edgeR
processamplicons
shrna
updated 8.5 years ago by
thomas.leete
• 0 • written 8.6 years ago by
Anne Deslattes Mays
▴ 10
0
votes
5
replies
2.8k
views
example fastq file, sampleAnnotaition and Hairpin file for shRNAseq/EdgeR tool
shRNAseq
edgeR
shRNA
updated 8.7 years ago by
Gordon Smyth
50k • written 8.7 years ago by
KB
▴ 50
5 results • Page
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Replies
Answer: all variables in design formula must be columns in colData (Deseq2) error
by
ATpoint
★ 4.1k
Your code is poorly readable. Suggest you select and then highlight with markdown using the `10101` button. Generally, colData(dds) must…
Answer: Subsetting RNAseq data | voomaByGroup()
by
Gordon Smyth
50k
Judging from your MDS plot, cell types 1 and 2 look radically different, so it would make perfect sense to analyse them separately. There's…
Answer: Numerical differences in DESeq2 output depending on different design matrix cons
by
Michael Love
42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs
by
Michael Love
42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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shepherl
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