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RPKM
•
reset
0
votes
0
replies
909
views
Tutorial:
Read data file containing both counts and annotation into edgeR
rpkm
edgeR
featureCounts
7 months ago
Gordon Smyth
50k
1
vote
4
replies
4.3k
views
Conversion from FPKM,RPKM to tpm
DESEQ2
fpkm
rpkm
tpm
2.6 years ago
Sandhiya
• 0
9
votes
10
replies
6.7k
views
How to get gene length for RPKM directly from DGEList object in latest edgeR?
Normalization
edgeR
RPKM
updated 13 months ago by
Chris
• 0 • written 3.5 years ago by
anikng
▴ 10
1
vote
5
replies
1.4k
views
bug in "dispersion" argument in edgeR - rpkmByGroup
edger
rpkm
updated 4.8 years ago by
rosehahn8583
• 0 • written 4.8 years ago by
dario.beraldi
• 0
7
votes
3
replies
3.2k
views
Log2(RPKM) counts in Bioconductor
rpkm
scater
calcaverage
R
expression
updated 5.0 years ago by
Aaron Lun
★ 28k • written 5.0 years ago by
kushshah
▴ 10
2
votes
1
reply
1.2k
views
Bioconductor with RPKM counts or Raw counts
singlecellexperiment
rpkm
normalization
qc
updated 5.0 years ago by
Aaron Lun
★ 28k • written 5.0 years ago by
kushshah
▴ 10
1
vote
1
reply
980
views
Generating RPKM data from dds (DESeq2 pipeline)
deseq2
dds
RPKM
updated 6.0 years ago by
Michael Love
41k • written 6.0 years ago by
harry.horsnell.17
• 0
32
votes
16
replies
17k
views
difference among tximport scaledTPM, lengthScaledTPM and the original TPM output by salmon/kallisto
tximport
deseq2
TPM
RPKM
rnaseq
updated 6.0 years ago by
luxeredias
▴ 20 • written 7.8 years ago by
tangming2005
▴ 190
3
votes
1
reply
1.2k
views
RMS question in MEDIPS
RMS
RPKM
MEDIPS
updated 6.2 years ago by
Lukas Chavez
▴ 570 • written 6.2 years ago by
enrique.yeh
▴ 10
2
votes
14
replies
7.5k
views
Calculating rpkm from counts data?
r
featurecounts
rpkm
tpm
edger
updated 14 months ago by
Chris
• 0 • written 6.7 years ago by
Biologist
▴ 110
3
votes
2
replies
1.6k
views
AnnotationHub: A RPKM data.frame of Epigenomics RoadMap Project seems strange
annotationhub
roadmap project
rpkm
data.frame
7.5 years ago
wcstcyx
▴ 30
4
votes
2
replies
5.2k
views
How to run the rpkm function of edgeR
edger
rpkm
updated 8.1 years ago by
Aaron Lun
★ 28k • written 8.1 years ago by
Gary
▴ 20
4
votes
10
replies
5.2k
views
Finding gene lengths of mm10 to calculate rpkm from count matrix of rna-seq dataset
rpkm
gene length
count matrix
edgeR
rsubread
8.5 years ago
AB
▴ 110
4
votes
1
reply
2.4k
views
Get source code for rpkm() function in edgeR
edgeR
rpkm
source
code
updated 9.0 years ago by
Martin Morgan
25k • written 9.0 years ago by
thibault.lorin
▴ 10
7
votes
4
replies
2.5k
views
Gene expression between two copies of same gene:use counts or RPKM or FPKM?
count
rnaseq
rpkm
fpkm
edgeR
updated 9.0 years ago by
Gordon Smyth
50k • written 9.0 years ago by
thibault.lorin
▴ 10
3
votes
3
replies
6.8k
views
Find DEG from RNA-seq: What if have only RPKM data?
deg
rna-seq
rpkm
updated 9.1 years ago by
b.nota
▴ 360 • written 9.1 years ago by
Yue Zhao
• 0
0
votes
5
replies
2.6k
views
count tables created with easyRNASeq and the rpkm() function from edgeR
easyrnaseq
edger
rpkm
updated 9.2 years ago by
Nicolas Delhomme
▴ 320 • written 9.2 years ago by
Sylvain Foisy
▴ 70
4
votes
4
replies
20k
views
edgeR rpkm function
edger
rpkm
updated 13 months ago by
Gordon Smyth
50k • written 9.2 years ago by
Makis Motakis
▴ 30
3
votes
2
replies
16k
views
how to calculate gene length to be used in rpkm() in edgeR
RNASeq
edgeR
rpkm
updated 12 months ago by
Gordon Smyth
50k • written 10.0 years ago by
shirley zhang
★ 1.0k
2
votes
1
reply
1.5k
views
Shoud I use "aligned reads" or total reads (aligned + unassigned) to the RPKM value?
rnaseq
R
rsubread
rpkm
updated 9.5 years ago by
James W. MacDonald
65k • written 9.5 years ago by
gustavoborin01
• 0
20 results • Page
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Replies
Comment: DESeq filtering specific to contrasts
by
Michael Love
41k
It will likely not filter it out, but really the per-dataset details would affect the results.
Comment: DESeq filtering specific to contrasts
by
Carlin95
• 0
Thanks for clarifying. Could I ask maybe one more thing for my sanity? Let's say you had a multi-factor experiment with contrasts including…
Comment: FilterByExpr low counts with small sample size
by
Jonathan
▴ 10
Thank you for your answer; However, I have some follow-up questions. Following up in In your [1-2-3 article][1], you say that > "... the…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa
by
Seyram M.
• 0
Thank you very much for your reply! I will do so. Kind regards, Seyram
Comment: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
by
isaac.vock
• 0
Thank you for your response. I can confirm that setting `-t exon` and/or removing `-s 1` and adding `-O` has no impact on the number of suc…
Votes
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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