Showing : RPKM • reset
0
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923
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Tutorial: Read data file containing both counts and annotation into edgeR
rpkm edgeR featureCounts
7 months ago Gordon Smyth 50k
1
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4
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4.3k
views
Conversion from FPKM,RPKM to tpm
DESEQ2 fpkm rpkm tpm
2.6 years ago Sandhiya • 0
9
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10
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6.8k
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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
1
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5
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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
2
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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
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
1
vote
1
reply
984
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Generating RPKM data from dds (DESeq2 pipeline)
deseq2 dds RPKM
updated 6.0 years ago by 41k • written 6.0 years ago by • 0
3
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1
reply
1.2k
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RMS question in MEDIPS
RMS RPKM MEDIPS
updated 6.2 years ago by ▴ 570 • written 6.2 years ago by ▴ 10
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
3
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2
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1.6k
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AnnotationHub: A RPKM data.frame of Epigenomics RoadMap Project seems strange
annotationhub roadmap project rpkm data.frame
7.5 years ago wcstcyx ▴ 30
32
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16
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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
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
4
votes
10
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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
4
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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
7
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4
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2.5k
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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
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
0
votes
5
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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
4
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4
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20k
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edgeR rpkm function
edger rpkm
updated 13 months ago by 50k • written 9.2 years ago by ▴ 30
2
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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
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2
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16k
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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
20 results • Page 1 of 1
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Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR) by Michael Love 41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Comment: Trying to use enrichGO by fernanda.backsouza ▴ 10
With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Answer: Opposite sign of LFC in count plots of DEGs (DESeq2) by swbarnes2 ★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error by James W. MacDonald 65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
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C: when to apply quantile normalization with voom in limma/voom framework with RNA-
A: How to know if I should use voomWithQualityWeights() or not?
A: Weird results (ribosomal proteins / Y-linked genes) in limma/voom
Answer: Log-cpm values from limma
Answer: Log-cpm values from limma
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