Showing : RPKM • reset
0
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897
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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
vote
4
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4.2k
views
Conversion from FPKM,RPKM to tpm
DESEQ2 fpkm rpkm tpm
2.6 years ago • updated 2.5 years ago Sandhiya • 0
9
votes
10
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6.7k
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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
vote
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
7
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3
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3.2k
views
Log2(RPKM) counts in Bioconductor
rpkm scater calcaverage R expression
updated 5.0 years ago by ★ 28k • written 5.0 years ago by ▴ 10
2
votes
1
reply
1.2k
views
Bioconductor with RPKM counts or Raw counts
singlecellexperiment rpkm normalization qc
updated 5.0 years ago by ★ 28k • written 5.0 years ago by ▴ 10
1
vote
1
reply
977
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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
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
3
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1
reply
1.2k
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RMS question in MEDIPS
RMS RPKM MEDIPS
updated 6.1 years ago by ▴ 570 • written 6.1 years ago by ▴ 10
2
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14
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7.5k
views
Calculating rpkm from counts data?
r featurecounts rpkm tpm edger
updated 13 months ago by • 0 • written 6.7 years ago by ▴ 110
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
4
votes
2
replies
5.2k
views
How to run the rpkm function of edgeR
edger rpkm
updated 8.1 years ago by ★ 28k • written 8.1 years ago by ▴ 20
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
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
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
3
votes
3
replies
6.7k
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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2.5k
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 ▴ 70
4
votes
4
replies
20k
views
edgeR rpkm function
edger rpkm
updated 13 months ago by 50k • written 9.2 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 12 months ago by 50k • written 10.0 years ago by ★ 1.0k
2
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1
reply
1.5k
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
20 results • Page 1 of 1
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Replies
Comment: DEG with low counts by Rajat • 0
Dear Dr. Michael Thanks for you quick reply. I appreciate it. Attached is the plotcounts for one gene. I am experiencing like this in oth…
Comment: Light difference when using coef vs omit a group when compare 3 groups. by Chris • 0
Hi Gordon, thank you so much for your guide! I check my data as you said there is no difference in my data. This is the MDS plot at genes l…
Comment: How to correct for known and surrogate variables in DESeq2? by Michael Love 41k
To question 3: if you model technical variation using only ~group vs ~1, then it will be correlated with known technical variables, which y…
Answer: flowStats Search Error by shepherl 3.8k
We are aware of an issue with bioconductor.org search and are investigating. We apologize for an inconvenience this is causing.
Comment: How to correct for known and surrogate variables in DESeq2? by nhaus ▴ 30
Hey Crystal, did you end up getting advice? I am facing the exact same questions that you are having right now. Would be very grateful if y…
Votes
Answer: Light difference when using coef vs omit a group when compare 3 groups.
C: Add new columns to DESeqResults from text file by matching rownames.
Answer: geneList error in clusterprofiler
Comment: Memory errors using read.bismark?
Comment: Not fully paired differential gene expression analysis
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