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JunctionSeq
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2
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1.1k
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Question: Error when running QoRTs for JunctionSeq
DEXSeq
JunctionSeq
RNAseq
QoRTs
3.1 years ago • updated 3.0 years ago
n.tear
▴ 20
0
votes
1
reply
793
views
JunctionSeq producing strangely large effect sizes for certain exon counting bins
junctionseq
splicing
RNAseq
DEXSeq
4.3 years ago
stuart
▴ 10
0
votes
1
reply
812
views
JunctionSeq Can't produce Summary Plots
JunctionSeq
6.9 years ago
rachelrodgers12
• 0
0
votes
0
replies
803
views
Setting relevel with the JunctionSeq package
junctionseq
relevel
reference
7.1 years ago
Assa Yeroslaviz
★ 1.5k
1
vote
0
replies
913
views
JunctionSeq on multiple conditions
junctionseq
qorts
multiple factor design
relevel
7.1 years ago
Assa Yeroslaviz
★ 1.5k
0
votes
1
reply
1.3k
views
JunctionSeq/DEXSeq: Dispersion plot looks strange (but is fine in DESeq2)
deseq2
junctionseq
dexseq
estimatedispersions
rnaseq
updated 7.3 years ago by
Steve Lianoglou
★ 13k • written 7.3 years ago by
l.frank
• 0
0
votes
0
replies
811
views
Problems running JunctionSeq
junctionseq
7.3 years ago
jbono
▴ 10
0
votes
0
replies
815
views
JunctionSeq pairwise contrast with a multi-level treatment
junctionseq
design and contrast matrix
7.4 years ago
stuart
• 0
8 results • Page
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Replies
Comment: DEG Filtering
by
Gordon Smyth
50k
RMA normalization is good but batch correction using NOISeq isn't right. Data shouldn't be batch corrected before the limma analysis and NO…
Answer: maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicat
by
snijesh
▴ 20
You can try: using `read.delim` or `fread`. ``` my_maf = data.table::fread("path/to/maf/sample.maf") my_maf = read.maf(maf = my_maf) …
Comment: DEG Filtering
by
Amit
• 0
Hi Gordon, Thank you for your response and advice. I want to analyze Dataset GSE18090 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi) whic…
Comment: edgeR, 3 x 2 design with a batch effect and contrasts
by
Gordon Smyth
50k
Yes, that is a quote from [A guide to creating design matrices for gene expression experiments](https://bioconductor.org/packages/release/w…
Comment: edgeR, 3 x 2 design with a batch effect and contrasts
by
JKim
• 0
Thank you. I think I found why the order matters. > Although an intercept-free design matrix has been coded using the 0+ notation, the in…
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C: How to check that the reads in two fastq files are in the same order
Answer: edgeR, 3 x 2 design with a batch effect and contrasts
Answer: Need help with creating and plotting temporal clustering analysis of DEGs
Answer: Problem converting msigdb Human symbols to Zebrafish in gmt format
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