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rpkm
•
reset
1
vote
4
replies
2.4k
views
Conversion from FPKM,RPKM to tpm
DESEQ2
fpkm
rpkm
tpm
16 months ago
Sandhiya
• 0
9
votes
8
replies
3.2k
views
How to get gene length for RPKM directly from DGEList object in latest edgeR?
Normalization
edgeR
RPKM
updated 2.3 years ago by
Gordon Smyth
47k • written 2.3 years ago by
anikng
▴ 10
1
vote
5
replies
933
views
bug in "dispersion" argument in edgeR - rpkmByGroup
edger
rpkm
updated 3.6 years ago by
rosehahn8583
• 0 • written 3.6 years ago by
dario.beraldi
• 0
6
votes
3
replies
2.0k
views
Log2(RPKM) counts in Bioconductor
rpkm
scater
calcaverage
R
expression
updated 3.8 years ago by
Aaron Lun
★ 28k • written 3.8 years ago by
kushshah
▴ 10
2
votes
1
reply
674
views
Bioconductor with RPKM counts or Raw counts
singlecellexperiment
rpkm
normalization
qc
updated 3.8 years ago by
Aaron Lun
★ 28k • written 3.8 years ago by
kushshah
▴ 10
1
vote
1
reply
646
views
Generating RPKM data from dds (DESeq2 pipeline)
deseq2
dds
RPKM
updated 4.7 years ago by
Michael Love
39k • written 4.7 years ago by
harry.horsnell.17
• 0
30
votes
16
replies
14k
views
difference among tximport scaledTPM, lengthScaledTPM and the original TPM output by salmon/kallisto
tximport
deseq2
TPM
RPKM
rnaseq
updated 4.8 years ago by
luxeredias
▴ 20 • written 6.6 years ago by
tangming2005
▴ 190
3
votes
1
reply
775
views
RMS question in MEDIPS
RMS
RPKM
MEDIPS
updated 4.9 years ago by
Lukas Chavez
▴ 570 • written 4.9 years ago by
enrique.yeh
▴ 10
2
votes
13
replies
5.5k
views
Calculating rpkm from counts data?
r
featurecounts
rpkm
tpm
edger
updated 5.5 years ago by
kristoffer.vittingseerup
▴ 20 • written 5.5 years ago by
Biologist
▴ 110
3
votes
2
replies
1.2k
views
AnnotationHub: A RPKM data.frame of Epigenomics RoadMap Project seems strange
annotationhub
roadmap project
rpkm
data.frame
6.3 years ago
wcstcyx
▴ 30
4
votes
2
replies
4.3k
views
How to run the rpkm function of edgeR
edger
rpkm
updated 6.9 years ago by
Aaron Lun
★ 28k • written 6.9 years ago by
Gary
▴ 20
4
votes
10
replies
4.1k
views
Finding gene lengths of mm10 to calculate rpkm from count matrix of rna-seq dataset
rpkm
gene length
count matrix
edgeR
rsubread
7.3 years ago
AB
▴ 110
4
votes
1
reply
1.9k
views
Get source code for rpkm() function in edgeR
edgeR
rpkm
source
code
updated 7.8 years ago by
Martin Morgan
25k • written 7.8 years ago by
thibault.lorin
▴ 10
7
votes
4
replies
1.9k
views
Gene expression between two copies of same gene:use counts or RPKM or FPKM?
count
rnaseq
rpkm
fpkm
edgeR
updated 7.8 years ago by
Gordon Smyth
47k • written 7.8 years ago by
thibault.lorin
▴ 10
3
votes
3
replies
5.7k
views
Find DEG from RNA-seq: What if have only RPKM data?
deg
rna-seq
rpkm
updated 7.9 years ago by
b.nota
▴ 360 • written 7.9 years ago by
Yue Zhao
• 0
0
votes
5
replies
2.0k
views
count tables created with easyRNASeq and the rpkm() function from edgeR
easyrnaseq
edger
rpkm
updated 7.9 years ago by
Nicolas Delhomme
▴ 320 • written 7.9 years ago by
Sylvain Foisy
▴ 30
4
votes
2
replies
16k
views
edgeR rpkm function
edger
rpkm
updated 8.0 years ago by
Gordon Smyth
47k • written 8.0 years ago by
Makis Motakis
▴ 30
3
votes
2
replies
14k
views
how to calculate gene length to be used in rpkm() in edgeR
RNASeq
edgeR
rpkm
updated 8.2 years ago by
Gordon Smyth
47k • written 8.7 years ago by
shirley zhang
★ 1.0k
2
votes
1
reply
1.3k
views
Shoud I use "aligned reads" or total reads (aligned + unassigned) to the RPKM value?
rnaseq
R
rsubread
rpkm
updated 8.3 years ago by
James W. MacDonald
62k • written 8.3 years ago by
gustavoborin01
• 0
19 results • Page
1 of 1
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Replies
Comment: How to normalize long-read RNA-seq data for comparison with short-reads
by
Bernardo
• 0
Just did that, thank you for the suggestion.
Comment: Empty ChipQC Report
by
Okan
• 0
Hi, I have the same issue. Have you found any solution or any reason why this is happening?
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper
by
Gordon Smyth
47k
Am I understanding correctly that you have 24 RNA-seq libraries in total, 6 from the pooled samples and 18 from regular samples with biolog…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper
by
k.roelfs
• 0
I'm sorry, I know it is kinda confusing... We have 6 pools in total: Phenotype A: T1a, T2, T1b, T1c Phenotype B: T1, T2 Each pool consist…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper
by
Gordon Smyth
47k
Sorry, I don't understand your experiment. You are reading the edgeR Section on on what to do without replicates, but your experiment appe…
Votes
Comment: How to normalize long-read RNA-seq data for comparison with short-reads
Volcano Plot in R
Answer: Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
Answer: Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
Answer: MA plot
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