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rpkm
•
reset
0
votes
0
replies
1.5k
views
Tutorial:
Read data file containing both counts and annotation into edgeR
rpkm
edgeR
featureCounts
15 months ago
Gordon Smyth
52k
1
vote
4
replies
5.1k
views
Conversion from FPKM,RPKM to tpm
DESEQ2
fpkm
rpkm
tpm
3.2 years ago
Sandhiya
• 0
9
votes
10
replies
8.3k
views
How to get gene length for RPKM directly from DGEList object in latest edgeR?
Normalization
edgeR
RPKM
updated 20 months ago by
Chris
▴ 20 • written 4.1 years ago by
anikng
▴ 10
1
vote
5
replies
1.7k
views
bug in "dispersion" argument in edgeR - rpkmByGroup
edger
rpkm
updated 5.5 years ago by
rosehahn8583
• 0 • written 5.5 years ago by
dario.beraldi
• 0
7
votes
3
replies
3.8k
views
Log2(RPKM) counts in Bioconductor
rpkm
scater
calcaverage
R
expression
updated 5.7 years ago by
Aaron Lun
★ 28k • written 5.7 years ago by
kushshah
▴ 10
2
votes
1
reply
1.5k
views
Bioconductor with RPKM counts or Raw counts
singlecellexperiment
rpkm
normalization
qc
updated 5.7 years ago by
Aaron Lun
★ 28k • written 5.7 years ago by
kushshah
▴ 10
1
vote
1
reply
1.2k
views
Generating RPKM data from dds (DESeq2 pipeline)
deseq2
dds
RPKM
updated 6.6 years ago by
Michael Love
43k • written 6.6 years ago by
harry.horsnell.17
• 0
32
votes
16
replies
19k
views
difference among tximport scaledTPM, lengthScaledTPM and the original TPM output by salmon/kallisto
tximport
deseq2
TPM
RPKM
rnaseq
updated 6.6 years ago by
luxeredias
▴ 20 • written 8.4 years ago by
tangming2005
▴ 200
3
votes
1
reply
1.4k
views
RMS question in MEDIPS
RMS
RPKM
MEDIPS
updated 6.8 years ago by
Lukas Chavez
▴ 570 • written 6.8 years ago by
enrique.yeh
▴ 10
2
votes
14
replies
8.6k
views
Calculating rpkm from counts data?
r
featurecounts
rpkm
tpm
edger
updated 21 months ago by
Chris
▴ 20 • written 7.3 years ago by
Biologist
▴ 120
3
votes
2
replies
1.8k
views
AnnotationHub: A RPKM data.frame of Epigenomics RoadMap Project seems strange
annotationhub
roadmap project
rpkm
data.frame
8.2 years ago • updated 8.1 years ago
wcstcyx
▴ 30
4
votes
2
replies
5.6k
views
How to run the rpkm function of edgeR
edger
rpkm
updated 8.8 years ago by
Aaron Lun
★ 28k • written 8.8 years ago by
Gary
▴ 20
4
votes
10
replies
5.7k
views
Finding gene lengths of mm10 to calculate rpkm from count matrix of rna-seq dataset
rpkm
gene length
count matrix
edgeR
rsubread
9.1 years ago
AB
▴ 110
4
votes
1
reply
2.5k
views
Get source code for rpkm() function in edgeR
edgeR
rpkm
source
code
updated 9.7 years ago by
Martin Morgan
25k • written 9.7 years ago by
thibault.lorin
▴ 10
7
votes
4
replies
2.8k
views
Gene expression between two copies of same gene:use counts or RPKM or FPKM?
count
rnaseq
rpkm
fpkm
edgeR
updated 9.7 years ago by
Gordon Smyth
52k • written 9.7 years ago by
thibault.lorin
▴ 10
3
votes
3
replies
7.4k
views
Find DEG from RNA-seq: What if have only RPKM data?
deg
rna-seq
rpkm
updated 9.7 years ago by
b.nota
▴ 370 • written 9.7 years ago by
Yue Zhao
• 0
0
votes
5
replies
2.8k
views
count tables created with easyRNASeq and the rpkm() function from edgeR
easyrnaseq
edger
rpkm
updated 9.8 years ago by
Nicolas Delhomme
▴ 320 • written 9.8 years ago by
Sylvain Foisy
▴ 80
4
votes
4
replies
22k
views
edgeR rpkm function
edger
rpkm
updated 20 months ago by
Gordon Smyth
52k • written 9.8 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 19 months ago by
Gordon Smyth
52k • written 10.6 years ago by
shirley zhang
★ 1.0k
2
votes
1
reply
1.7k
views
Shoud I use "aligned reads" or total reads (aligned + unassigned) to the RPKM value?
rnaseq
R
rsubread
rpkm
updated 10.1 years ago by
James W. MacDonald
67k • written 10.1 years ago by
gustavoborin01
• 0
20 results • Page
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Comment: How to annotate a limma Elist raw class object with an annotation file
by
James W. MacDonald
67k
Oh right. My bad. Good for you though, figuring out that it's ENTREZID, not ENTREZGENE. You did a good job of reading the error message in …
Comment: Differential Expression Genes as Independent Variables
by
James W. MacDonald
67k
Both true, so a poor suggestion on my part. I am also unclear as to how one would use a single observation (the gene expression measures)…
Answer: How to annotate a limma Elist raw class object with an annotation file
by
giulia.gentile
• 0
Good afternoon, Thank you for your explanation and suggestion to overcome the issue by annotating directly from the genome-wide annotation…
Comment: scuttle::perFeatureQCMetrics runs very slow for big scRNA-seq data
by
Aaron Lun
★ 28k
IIRC loading ~million cells into memory took about 3-5 minutes, but that was with a rather slow filesystem (HDD on a HPC), so YMMV dependin…
Comment: Differential Expression Genes as Independent Variables
by
Gordon Smyth
52k
Does not allow mixed models. And is for a different purpose to what your aims seem to be: it's purely for prediction rather than for testin…
Votes
conumee with Infinium MethylationEPIC v2.0
A: How to bin a GRanges to small bins
C: How to bin a GRanges to small bins
C: How to bin a GRanges to small bins
A: deseq2 filter the low counts
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mohammedtoufiq91
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★ 3.4k
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HS
▴ 10
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James W. MacDonald
67k
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shepherl
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