Showing : rpkm • reset
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Tutorial: Read data file containing both counts and annotation into edgeR
rpkm edgeR featureCounts
14 months ago Gordon Smyth 51k
1
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4
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5.0k
views
Conversion from FPKM,RPKM to tpm
DESEQ2 fpkm rpkm tpm
3.1 years ago Sandhiya • 0
9
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10
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8.2k
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How to get gene length for RPKM directly from DGEList object in latest edgeR?
Normalization edgeR RPKM
updated 20 months ago by ▴ 20 • written 4.0 years ago by ▴ 10
1
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5
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1.7k
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bug in "dispersion" argument in edgeR - rpkmByGroup
edger rpkm
updated 5.4 years ago by • 0 • written 5.4 years ago by • 0
7
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3
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3.8k
views
Log2(RPKM) counts in Bioconductor
rpkm scater calcaverage R expression
updated 5.6 years ago by ★ 28k • written 5.6 years ago by ▴ 10
2
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1
reply
1.5k
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Bioconductor with RPKM counts or Raw counts
singlecellexperiment rpkm normalization qc
updated 5.6 years ago by ★ 28k • written 5.6 years ago by ▴ 10
1
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1
reply
1.2k
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Generating RPKM data from dds (DESeq2 pipeline)
deseq2 dds RPKM
updated 6.5 years ago by 42k • written 6.5 years ago by • 0
32
votes
16
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19k
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difference among tximport scaledTPM, lengthScaledTPM and the original TPM output by salmon/kallisto
tximport deseq2 TPM RPKM rnaseq
updated 6.5 years ago by ▴ 20 • written 8.3 years ago by ▴ 200
3
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1
reply
1.3k
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RMS question in MEDIPS
RMS RPKM MEDIPS
updated 6.7 years ago by ▴ 570 • written 6.7 years ago by ▴ 10
2
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14
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8.5k
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Calculating rpkm from counts data?
r featurecounts rpkm tpm edger
updated 20 months ago by ▴ 20 • written 7.2 years ago by ▴ 120
3
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2
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1.8k
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AnnotationHub: A RPKM data.frame of Epigenomics RoadMap Project seems strange
annotationhub roadmap project rpkm data.frame
8.1 years ago • updated 8.0 years ago wcstcyx ▴ 30
4
votes
2
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5.6k
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How to run the rpkm function of edgeR
edger rpkm
updated 8.7 years ago by ★ 28k • written 8.7 years ago by ▴ 20
4
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10
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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
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1
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2.5k
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Get source code for rpkm() function in edgeR
edgeR rpkm source code
updated 9.6 years ago by 25k • written 9.6 years ago by ▴ 10
7
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4
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2.8k
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Gene expression between two copies of same gene:use counts or RPKM or FPKM?
count rnaseq rpkm fpkm edgeR
updated 9.6 years ago by 51k • written 9.6 years ago by ▴ 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 ▴ 370 • written 9.7 years ago by • 0
0
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5
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2.8k
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count tables created with easyRNASeq and the rpkm() function from edgeR
easyrnaseq edger rpkm
updated 9.7 years ago by ▴ 320 • written 9.7 years ago by ▴ 80
4
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4
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21k
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edgeR rpkm function
edger rpkm
updated 20 months ago by 51k • written 9.8 years ago by ▴ 30
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 18 months ago by 51k • written 10.5 years ago by ★ 1.0k
2
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1
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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 67k • written 10.0 years ago by • 0
20 results • Page 1 of 1
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Comment: Differential Expression Analysis with unbalanced batches without replication bet by Thili • 0
Thank you for your reply. I currently have batch-corrected data processed with scvi-tools (specifically, totalvi) and have followed the sam…
Comment: Problem at champ.load by andrew.gibbons • 0
I'd love to know if anyone has a workaround too. I've tried rolling back ChAMP and R to the previous versions that others have said work wi…
Comment: ESTMATE, MCPcounter, EPIC, xCell input by Kang • 0
These are not, as far as I know, bioconductor packages. You should query on the websites for those specific software programs. @[mapquest][…
Comment: Robust way of dealing with low number of samples for Differential Gene Expressio by Kang • 0
I believe that pseudo-bulking is a strong way to approach DE, as long as it is possible to reliably identify the cell type across data and …
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Thank you for the reply. I tried swapping columns before asking, it made no difference. head(keggframeData) path_id kegg…
Votes
A: Up/Down Regulated GeneList from edgeR and R
A: Up/Down Regulated GeneList from edgeR and R
A: Down/Up-regulated genes asymmetry in edgeR differential expression analysis
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