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RSEM
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reset
1
vote
2
replies
154
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Problem in running DESeq from expected count data of Transcriptome by Trinity followed by RSEM
Tissue
Spati
RSEM
deno
DEseq2
23 days ago • updated 22 days ago
shashank
• 0
1
vote
4
replies
245
views
How to deal with the negative values from EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2 when DEGs
limma
edgeR
RSEM
updated 10 weeks ago by
Gordon Smyth
47k • written 10 weeks ago by
Yang Shi
▴ 10
1
vote
2
replies
167
views
Differential expression analysis based on EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2
DESeq2
limma
edgeR
RSEM
11 weeks ago
Yang Shi
▴ 10
2
votes
3
replies
512
views
Error while reading rsem files in tximport
DESeq2
tximport
rsem
RNASeq
tximportData
6 months ago
mohammedtoufiq91
▴ 10
0
votes
3
replies
347
views
Differential Expression Analysis on RNAseq - RSEM expected_count from UCSC RNA-Seq toil recompute
DESeq2
Toil
RSEM
7 months ago
Niveditha
▴ 20
4
votes
5
replies
1.0k
views
Which is the best type of data for correlation or survival analysis
TPM
RNASeq
RSEM
DESeq2
updated 9 months ago by
Michael Love
40k • written 10 months ago by
Yang Shi
▴ 10
5
votes
9
replies
922
views
GSVA perfomed on RSEM Expected Count data
GSVA
RNA-Seq
RSEM
Expected_Count
10 months ago
Yang Shi
▴ 10
5
votes
6
replies
761
views
Removing the duplicated genes before limma::voom by using limma::avereps
RSEM
avereps
voom
limma
RNASeq
10 months ago
Yang Shi
▴ 10
2
votes
4
replies
515
views
Doing normalization when using voom for DEG analysis?
limma
RSEM
voom
Normalization
10 months ago
Yang Shi
▴ 10
2
votes
8
replies
846
views
RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM
tximport
scRNAseq
DESeq2
11 months ago
Kelen
▴ 10
6
votes
13
replies
3.4k
views
How to use RSEM value to find differentially expressed genes
RSEM
limma
edgeR
voom
normalization
updated 10 months ago by
Gordon Smyth
47k • written 2.8 years ago by
harelarik
▴ 60
11 results • Page
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Comment: Use with_go along with other filters in getBM function
by
RuBBiT0
▴ 10
Thank you! I think that makes much sense to me.
Comment: Interpret plot from DiffBind
by
Rory Stark
★ 4.9k
Not necessarily. It look to me like there is reconfiguring going on, with some chromatin that was open in the control becoming closed (the …
Comment: Interpret plot from DiffBind
by
Chris
• 0
Thanks Rory! So that means the diseased sample has chromatin more open then the control one, is that correct?
Answer: List of Deprecated Packages for Bioc3.17
by
shepherl
3.5k
lfa and gcatest have been reinstated.
Comment: Remove duplicate genera in DEseq output?
by
Lluís Revilla Sancho
▴ 710
How is your data before calculating the deg_DESeq? I see you use `phyloseq_to_deseq2` which should work well, but have you double checked t…
Votes
Comment: Interpret plot from DiffBind
Answer: Use with_go along with other filters in getBM function
Answer: Use with_go along with other filters in getBM function
Answer: Interpret plot from DiffBind
A: Generating a proper TxDb instance from NCBI GFF Annotations File
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