Showing : RPKM • reset
0
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0
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1.5k
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Tutorial: Read data file containing both counts and annotation into edgeR
rpkm edgeR featureCounts
16 months ago • updated 15 months ago Gordon Smyth 52k
1
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4
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5.2k
views
Conversion from FPKM,RPKM to tpm
DESEQ2 fpkm rpkm tpm
3.2 years ago Sandhiya • 0
9
votes
10
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8.4k
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How to get gene length for RPKM directly from DGEList object in latest edgeR?
Normalization edgeR RPKM
updated 21 months ago by ▴ 20 • written 4.2 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 5.5 years ago by • 0 • written 5.5 years ago by • 0
7
votes
3
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3.9k
views
Log2(RPKM) counts in Bioconductor
rpkm scater calcaverage R expression
updated 5.7 years ago by ★ 28k • written 5.7 years ago by ▴ 10
2
votes
1
reply
1.5k
views
Bioconductor with RPKM counts or Raw counts
singlecellexperiment rpkm normalization qc
updated 5.7 years ago by ★ 28k • written 5.7 years ago by ▴ 10
1
vote
1
reply
1.3k
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Generating RPKM data from dds (DESeq2 pipeline)
deseq2 dds RPKM
updated 6.6 years ago by 43k • written 6.6 years ago by • 0
32
votes
16
replies
19k
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difference among tximport scaledTPM, lengthScaledTPM and the original TPM output by salmon/kallisto
tximport deseq2 TPM RPKM rnaseq
updated 6.7 years ago by ▴ 20 • written 8.5 years ago by ▴ 200
3
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1
reply
1.4k
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RMS question in MEDIPS
RMS RPKM MEDIPS
updated 6.8 years ago by ▴ 570 • written 6.8 years ago by ▴ 10
2
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14
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8.6k
views
Calculating rpkm from counts data?
r featurecounts rpkm tpm edger
updated 22 months ago by ▴ 20 • written 7.4 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
8.2 years ago wcstcyx ▴ 30
4
votes
2
replies
5.7k
views
How to run the rpkm function of edgeR
edger rpkm
updated 8.8 years ago by ★ 28k • written 8.8 years ago by ▴ 20
4
votes
10
replies
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
9.2 years ago AB ▴ 110
4
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1
reply
2.6k
views
Get source code for rpkm() function in edgeR
edgeR rpkm source code
updated 9.7 years ago by 25k • written 9.7 years ago by ▴ 10
7
votes
4
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2.8k
views
Gene expression between two copies of same gene:use counts or RPKM or FPKM?
count rnaseq rpkm fpkm edgeR
updated 9.7 years ago by 52k • written 9.7 years ago by ▴ 10
3
votes
3
replies
7.4k
views
Find DEG from RNA-seq: What if have only RPKM data?
deg rna-seq rpkm
updated 9.8 years ago by ▴ 370 • written 9.8 years ago by • 0
0
votes
5
replies
2.8k
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count tables created with easyRNASeq and the rpkm() function from edgeR
easyrnaseq edger rpkm
updated 9.8 years ago by ▴ 320 • written 9.9 years ago by ▴ 80
4
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4
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22k
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edgeR rpkm function
edger rpkm
updated 21 months ago by 52k • written 9.9 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 20 months ago by 52k • written 10.6 years ago by ★ 1.0k
2
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1
reply
1.7k
views
Shoud I use "aligned reads" or total reads (aligned + unassigned) to the RPKM value?
rnaseq R rsubread rpkm
updated 10.2 years ago by 67k • written 10.2 years ago by • 0
20 results • Page 1 of 1
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Replies
Comment: Cross-validation with multiple control subgroups in limma by Ali Barry ▴ 40
Thanks so much for taking the time here, the insights are much appreciated. I suspected I'd have to ad hoc compare results if I did repeat …
Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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