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RPKM
•
reset
0
votes
0
replies
1.4k
views
Tutorial:
Read data file containing both counts and annotation into edgeR
rpkm
edgeR
featureCounts
14 months ago
Gordon Smyth
51k
1
vote
4
replies
5.0k
views
Conversion from FPKM,RPKM to tpm
DESEQ2
fpkm
rpkm
tpm
3.1 years ago
Sandhiya
• 0
9
votes
10
replies
8.2k
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 5.4 years ago by
rosehahn8583
• 0 • written 5.4 years ago by
dario.beraldi
• 0
7
votes
3
replies
3.8k
views
Log2(RPKM) counts in Bioconductor
rpkm
scater
calcaverage
R
expression
updated 5.6 years ago by
Aaron Lun
★ 28k • written 5.6 years ago by
kushshah
▴ 10
2
votes
1
reply
1.5k
views
Bioconductor with RPKM counts or Raw counts
singlecellexperiment
rpkm
normalization
qc
updated 5.6 years ago by
Aaron Lun
★ 28k • written 5.6 years ago by
kushshah
▴ 10
1
vote
1
reply
1.2k
views
Generating RPKM data from dds (DESeq2 pipeline)
deseq2
dds
RPKM
updated 6.5 years ago by
Michael Love
42k • written 6.5 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 8.3 years ago by
tangming2005
▴ 200
3
votes
1
reply
1.3k
views
RMS question in MEDIPS
RMS
RPKM
MEDIPS
updated 6.7 years ago by
Lukas Chavez
▴ 570 • written 6.7 years ago by
enrique.yeh
▴ 10
2
votes
14
replies
8.5k
views
Calculating rpkm from counts data?
r
featurecounts
rpkm
tpm
edger
updated 20 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
8.1 years ago
wcstcyx
▴ 30
4
votes
2
replies
5.6k
views
How to run the rpkm function of edgeR
edger
rpkm
updated 8.7 years ago by
Aaron Lun
★ 28k • written 8.7 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 9.6 years ago by
Martin Morgan
25k • written 9.6 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 9.6 years ago by
Gordon Smyth
51k • written 9.6 years ago by
thibault.lorin
▴ 10
3
votes
3
replies
7.3k
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 9.7 years ago by
Nicolas Delhomme
▴ 320 • written 9.7 years ago by
Sylvain Foisy
▴ 80
4
votes
4
replies
21k
views
edgeR rpkm function
edger
rpkm
updated 20 months ago by
Gordon Smyth
51k • 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
51k • written 10.5 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 10.0 years ago by
James W. MacDonald
67k • written 10.1 years ago by
gustavoborin01
• 0
20 results • Page
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Comment: installation error for BiocNeighbors package
by
育
• 0
omitted error2 ~~~ /home/ikutsu/Tsuchiya_NGS/local/include/c++/13.2.0/bits/new_allocator.h: In instantiation of 'void std::__new_allocat…
Comment: installation error for BiocNeighbors package
by
育
• 0
omitted error1 ~~~ /home/ikutsu/Tsuchiya_NGS/local/bin/g++ -std=gnu++17 -fPIC -std=gnu++17 -I"/home/ikutsu/Tsuchiya_NGS/local/lib64/R/i…
Comment: DESeq2 interaction between cancer cells and microenvironment cells
by
monkeymartgameaz
• 0
This is healthy for you. It is your priorities that matter, not those activities you believe you cannot profit from. It is always wise to a…
Answer: Is it possible to parallelise saveHDF5SummarizedExperiment
by
Hervé Pagès
16k
Hi Stefano, Unfortunately HDF5 doesn't support concurrent writing so parallelising is not an option. A few things that maybe could help: …
Comment: incomplete official symbol mitochondrial genes in org.Hs.eg.db?
by
James W. MacDonald
67k
It's a simple two-liner in [getsrc.sh][1] ``` awk -F'\t' 'BEGIN {OFS=FS} {if($3 != $11 && $11 != "-") $3 = $11; print $0}' gene_info > tmp…
Votes
Comment: incomplete official symbol mitochondrial genes in org.Hs.eg.db?
Answer: Supercells with Basilisk fails for dtype('float64') to dtype('int64') conversion
A: GOseq analysis with only upregulated or downregulated genes
A: GOseq analysis with only upregulated or downregulated genes
Answer: Properly constructing a hypergeometric test
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