Showing : RPKM • reset
0
votes
0
replies
1.6k
views
Tutorial: Read data file containing both counts and annotation into edgeR
rpkm edgeR featureCounts
17 months ago Gordon Smyth 52k
1
vote
4
replies
5.4k
views
Conversion from FPKM,RPKM to tpm
DESEQ2 fpkm rpkm tpm
3.4 years ago Sandhiya • 0
9
votes
10
replies
8.7k
views
How to get gene length for RPKM directly from DGEList object in latest edgeR?
Normalization edgeR RPKM
updated 23 months ago by ▴ 20 • written 4.3 years ago by ▴ 10
1
vote
5
replies
1.7k
views
bug in "dispersion" argument in edgeR - rpkmByGroup
edger rpkm
updated 5.7 years ago by • 0 • written 5.7 years ago by • 0
7
votes
3
replies
4.0k
views
Log2(RPKM) counts in Bioconductor
rpkm scater calcaverage R expression
updated 5.9 years ago by ★ 28k • written 5.9 years ago by ▴ 10
2
votes
1
reply
1.6k
views
Bioconductor with RPKM counts or Raw counts
singlecellexperiment rpkm normalization qc
updated 5.9 years ago by ★ 28k • written 5.9 years ago by ▴ 10
1
vote
1
reply
1.3k
views
Generating RPKM data from dds (DESeq2 pipeline)
deseq2 dds RPKM
updated 6.8 years ago by 43k • written 6.8 years ago by • 0
32
votes
16
replies
20k
views
difference among tximport scaledTPM, lengthScaledTPM and the original TPM output by salmon/kallisto
tximport deseq2 TPM RPKM rnaseq
updated 6.8 years ago by ▴ 20 • written 8.6 years ago by ▴ 200
3
votes
1
reply
1.4k
views
RMS question in MEDIPS
RMS RPKM MEDIPS
updated 7.0 years ago by ▴ 570 • written 7.0 years ago by ▴ 10
2
votes
14
replies
8.8k
views
Calculating rpkm from counts data?
r featurecounts rpkm tpm edger
updated 24 months ago by ▴ 20 • written 7.5 years ago by ▴ 120
3
votes
2
replies
1.9k
views
AnnotationHub: A RPKM data.frame of Epigenomics RoadMap Project seems strange
annotationhub roadmap project rpkm data.frame
8.4 years ago • updated 8.3 years ago wcstcyx ▴ 30
4
votes
2
replies
5.8k
views
How to run the rpkm function of edgeR
edger rpkm
updated 9.0 years ago by ★ 28k • written 9.0 years ago by ▴ 20
4
votes
10
replies
5.8k
views
Finding gene lengths of mm10 to calculate rpkm from count matrix of rna-seq dataset
rpkm gene length count matrix edgeR rsubread
9.3 years ago AB ▴ 110
4
votes
1
reply
2.6k
views
Get source code for rpkm() function in edgeR
edgeR rpkm source code
updated 9.9 years ago by 25k • written 9.9 years ago by ▴ 10
7
votes
4
replies
2.9k
views
Gene expression between two copies of same gene:use counts or RPKM or FPKM?
count rnaseq rpkm fpkm edgeR
updated 9.9 years ago by 52k • written 9.9 years ago by ▴ 10
3
votes
3
replies
7.6k
views
Find DEG from RNA-seq: What if have only RPKM data?
deg rna-seq rpkm
updated 9.9 years ago by ▴ 370 • written 9.9 years ago by • 0
0
votes
5
replies
2.9k
views
count tables created with easyRNASeq and the rpkm() function from edgeR
easyrnaseq edger rpkm
updated 10.0 years ago by ▴ 320 • written 10.0 years ago by ▴ 80
4
votes
4
replies
22k
views
edgeR rpkm function
edger rpkm
updated 23 months ago by 52k • written 10.0 years ago by ▴ 30
3
votes
2
replies
16k
views
how to calculate gene length to be used in rpkm() in edgeR
RNASeq edgeR rpkm
updated 22 months ago by 52k • written 10.8 years ago by ★ 1.0k
2
votes
1
reply
1.8k
views
Shoud I use "aligned reads" or total reads (aligned + unassigned) to the RPKM value?
rnaseq R rsubread rpkm
updated 10.3 years ago by 68k • written 10.3 years ago by • 0
20 results • Page 1 of 1
Recent ...
Replies
Answer: SingleR with multiple single cell references by Aaron Lun ★ 28k
> Is it necessary to piece together the individual steps manually (e.g. aggregateReference, trainSingleR, classifySingleR, combineRecompute…
Answer: Automatically install dependencies by ATpoint ★ 4.7k
The BiocManager, which is sort of an extended wrapper around `install.packages`, installs all R dependencies. If you see errors then this i…
Answer: To count or not to count multi-overlapping reads? by Gordon Smyth 52k
> How does it handle reads that map to a gene that is located in a region that also has another gene but on the alternate strand? Overlapp…
Comment: Weird p-values using DESeq2? by ATpoint ★ 4.7k
This does not look like normalized counts but raw counts. Consider using `counts(dds, normalized = TRUE)` or the output of `normTransform()…
Answer: Weird p-values using DESeq2? by Wolfgang Huber ★ 13k
Dear Ingrid, thank you for asking. Can you provide the input count matrix (you can "pseudonymize" the biological conditions and the gene n…
Votes
A: Fraction count for multi mapping reads; how to generate input file for Deseq2 fo
Comment: Weird p-values using DESeq2?
Comment: Overcoming confounding in batch effect correction
Answer: Store Matrix in DataFrame Cell
Answer: enrichGOgradient color change
Awards • All
Popular Question to maltethodberg ▴ 180
Popular Question to abadgerw • 0
Popular Question to Jim Nemesh ▴ 10
Popular Question to Wolfgang Huber ★ 13k
Teacher to James W. MacDonald 68k
Locations • All
Hong Kong, 27 minutes ago
UPF, Barcelona, Spain, 2 hours ago
Pittsburgh, United States, 3 hours ago
United Kingdom, 4 hours ago
Finland, 5 hours ago
Traffic: 1112 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6