Showing : rpkm • reset
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Tutorial: Read data file containing both counts and annotation into edgeR
rpkm edgeR featureCounts
2.1 years ago Gordon Smyth 53k
1
vote
4
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5.9k
views
Conversion from FPKM,RPKM to tpm
DESEQ2 fpkm rpkm tpm
4.0 years ago Sandhiya • 0
9
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10
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9.6k
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How to get gene length for RPKM directly from DGEList object in latest edgeR?
Normalization edgeR RPKM
updated 2.6 years ago by ▴ 20 • written 5.0 years ago by ▴ 10
1
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5
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1.9k
views
bug in "dispersion" argument in edgeR - rpkmByGroup
edger rpkm
updated 6.3 years ago by • 0 • written 6.3 years ago by • 0
7
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3
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4.5k
views
Log2(RPKM) counts in Bioconductor
rpkm scater calcaverage R expression
updated 6.5 years ago by ★ 29k • written 6.5 years ago by ▴ 10
2
votes
1
reply
1.9k
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Bioconductor with RPKM counts or Raw counts
singlecellexperiment rpkm normalization qc
updated 6.5 years ago by ★ 29k • written 6.5 years ago by ▴ 10
1
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1
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1.5k
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Generating RPKM data from dds (DESeq2 pipeline)
deseq2 dds RPKM
updated 7.4 years ago by 43k • written 7.4 years ago by • 0
32
votes
16
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21k
views
difference among tximport scaledTPM, lengthScaledTPM and the original TPM output by salmon/kallisto
tximport deseq2 TPM RPKM rnaseq
updated 7.5 years ago by ▴ 20 • written 9.3 years ago by ▴ 200
3
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1
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1.6k
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RMS question in MEDIPS
RMS RPKM MEDIPS
updated 7.6 years ago by ▴ 570 • written 7.6 years ago by ▴ 10
2
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14
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9.6k
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Calculating rpkm from counts data?
r featurecounts rpkm tpm edger
updated 2.6 years ago by ▴ 20 • written 8.2 years ago by ▴ 120
3
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2
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2.1k
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AnnotationHub: A RPKM data.frame of Epigenomics RoadMap Project seems strange
annotationhub roadmap project rpkm data.frame
9.0 years ago wcstcyx ▴ 30
4
votes
2
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6.0k
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How to run the rpkm function of edgeR
edger rpkm
updated 9.6 years ago by ★ 29k • written 9.6 years ago by ▴ 20
4
votes
10
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6.2k
views
Finding gene lengths of mm10 to calculate rpkm from count matrix of rna-seq dataset
rpkm gene length count matrix edgeR rsubread
10.0 years ago AB ▴ 110
4
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1
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2.8k
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Get source code for rpkm() function in edgeR
edgeR rpkm source code
updated 10.5 years ago by 25k • written 10.5 years ago by ▴ 10
7
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4
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3.2k
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Gene expression between two copies of same gene:use counts or RPKM or FPKM?
count rnaseq rpkm fpkm edgeR
updated 10.5 years ago by 53k • written 10.5 years ago by ▴ 10
3
votes
3
replies
8.0k
views
Find DEG from RNA-seq: What if have only RPKM data?
deg rna-seq rpkm
updated 10.6 years ago by ▴ 370 • written 10.6 years ago by • 0
0
votes
5
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3.2k
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count tables created with easyRNASeq and the rpkm() function from edgeR
easyrnaseq edger rpkm
updated 10.6 years ago by ▴ 320 • written 10.7 years ago by ▴ 80
4
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4
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23k
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edgeR rpkm function
edger rpkm
updated 2.6 years ago by 53k • written 10.7 years ago by ▴ 30
3
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2
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17k
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how to calculate gene length to be used in rpkm() in edgeR
RNASeq edgeR rpkm
updated 2.5 years ago by 53k • written 11.4 years ago by ★ 1.0k
2
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1
reply
1.9k
views
Shoud I use "aligned reads" or total reads (aligned + unassigned) to the RPKM value?
rnaseq R rsubread rpkm
updated 11.0 years ago by 68k • written 11.0 years ago by • 0
20 results • Page 1 of 1
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Comment: Help with defining groups by Phinney, Brett ▴ 10
I got it working , thank you!!!
Comment: Check removeBatchEffect effectiveness by massimo • 0
I would kindly ask for additional support. When not including the design_timepoint argument in removeBatchEffect and thus keeping the inter…
Comment: Error Loading Experiment from SimBenchData Package by ksankaran • 0
Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset? by ATpoint ★ 5.0k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by ATpoint ★ 5.0k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Votes
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Answer: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
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