Showing : RPKM • reset
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
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 ▴ 320 • written 9.2 years ago by ▴ 80
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 ▴ 20 • written 7.8 years ago by ▴ 190
4
votes
4
replies
20k
views
edgeR rpkm function
edger rpkm
updated 13 months ago by 50k • written 9.2 years ago by ▴ 30
2
votes
14
replies
7.5k
views
Calculating rpkm from counts data?
r featurecounts rpkm tpm edger
updated 14 months ago by • 0 • written 6.7 years ago by ▴ 110
9
votes
10
replies
6.8k
views
How to get gene length for RPKM directly from DGEList object in latest edgeR?
Normalization edgeR RPKM
updated 13 months ago by • 0 • written 3.5 years ago by ▴ 10
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 50k • written 10.0 years ago by ★ 1.0k
3
votes
1
reply
1.2k
views
RMS question in MEDIPS
RMS RPKM MEDIPS
updated 6.2 years ago by ▴ 570 • written 6.2 years ago by ▴ 10
1
vote
1
reply
983
views
Generating RPKM data from dds (DESeq2 pipeline)
deseq2 dds RPKM
updated 6.0 years ago by 41k • written 6.0 years ago by • 0
7
votes
3
replies
3.2k
views
Log2(RPKM) counts in Bioconductor
rpkm scater calcaverage R expression
updated 5.1 years ago by ★ 28k • written 5.1 years ago by ▴ 10
2
votes
1
reply
1.3k
views
Bioconductor with RPKM counts or Raw counts
singlecellexperiment rpkm normalization qc
updated 5.1 years ago by ★ 28k • written 5.1 years ago by ▴ 10
1
vote
5
replies
1.4k
views
bug in "dispersion" argument in edgeR - rpkmByGroup
edger rpkm
updated 4.8 years ago by • 0 • written 4.8 years ago by • 0
1
vote
4
replies
4.3k
views
Conversion from FPKM,RPKM to tpm
DESEQ2 fpkm rpkm tpm
2.6 years ago Sandhiya • 0
2
votes
1
reply
1.6k
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 65k • written 9.5 years ago by • 0
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 ▴ 360 • written 9.1 years ago by • 0
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 50k • written 9.0 years ago by ▴ 10
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 25k • written 9.0 years ago by ▴ 10
4
votes
2
replies
5.2k
views
How to run the rpkm function of edgeR
edger rpkm
updated 8.2 years ago by ★ 28k • written 8.2 years ago by ▴ 20
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
0
votes
0
replies
916
views
Tutorial: Read data file containing both counts and annotation into edgeR
rpkm edgeR featureCounts
7 months ago Gordon Smyth 50k
20 results • Page 1 of 1
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Replies
Comment: minfi::read.metharray.exp by clacarion • 0
I think its work with `read.metharray.sheet` ```r > sheet <- read.metharray.sheet("/Users/clarachretienneau/Desktop/clock_epigenetic/PJ120…
Comment: minfi::read.metharray.exp by clacarion • 0
Thank you for your response Basti ! I add all the idat files in a unique folder called "idat" and add it in my path ```r > list.files("…
Answer: List of Deprecated Packages for Bioc3.19 by shepherl 3.8k
singleCellTK has been fixed and will remain in Bioconductor
Comment: Trying to use enrichGO by fernanda.backsouza ▴ 10
Yes, I'm working only with genes from terpenoids pathway (14 genes), so I can't use enrichGO? Can you recommend a package or something like…
Comment: Trying to use enrichGO by fernanda.backsouza ▴ 10
Your awnser at Cannabis orgDb solve my problems using enrichGO by far. I'm underdegree biotechnology student, and I learning bioinformatic…
Votes
Answer: How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
Answer: minfi::read.metharray.exp
Comment: Trying to use enrichGO
Answer: Cannabis OrgDb
DESeq2: How to find out how well the model fits the data?
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