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tpm
•
reset
16
votes
25
replies
3.1k
views
dtuScaledTPM vs lengthScaledTPM in DTU analysis
tximport
dtu
salmon
TPM
rnaseqDTU
written 5.1 years ago by
fiona.dick91
▴ 60
2
votes
18
replies
3.5k
views
Using tximport on rsem files produces error while trying to read in files
R
tximport
rnaseq
tpm
rsem
6.1 years ago
stephan.emmrich
▴ 10
33
votes
16
replies
40k
views
Differential expression analysis starting from TPM data
R
TPM
updated 6.8 years ago by
Gordon Smyth
50k • written 6.8 years ago by
cahidora
▴ 90
32
votes
16
replies
18k
views
difference among tximport scaledTPM, lengthScaledTPM and the original TPM output by salmon/kallisto
tximport
deseq2
TPM
RPKM
rnaseq
updated 6.1 years ago by
luxeredias
▴ 20 • written 7.9 years ago by
tangming2005
▴ 190
2
votes
14
replies
7.6k
views
Calculating rpkm from counts data?
r
featurecounts
rpkm
tpm
edger
updated 15 months ago by
Chris
▴ 10 • written 6.8 years ago by
Biologist
▴ 110
5
votes
8
replies
1.8k
views
Unexpected results while analyzing a subset of genes in GEO RNAseq dataset containing TPM values
R
limma
TPM
rnaseq
differential expression
updated 4.6 years ago by
Steve Lianoglou
★ 13k • written 4.6 years ago by
atakanekiz
▴ 30
6
votes
8
replies
2.8k
views
Use of pseudoalignment estimated counts as input to edgeR and Limma-Voom
RNASeq-quantification
edgeR
TPM
updated 5.3 years ago by
Gordon Smyth
50k • written 5.3 years ago by
raf4
▴ 20
2
votes
5
replies
11k
views
Normalization of RNA-seq data: between samples and within samples
rnaseq
normalization
tpm
tmm
8.6 years ago
nickbern92
• 0
4
votes
5
replies
2.2k
views
Which is the best type of data for correlation or survival analysis
TPM
RNASeq
RSEM
DESeq2
updated 21 months ago by
Michael Love
42k • written 21 months ago by
Yang Shi
▴ 10
1
vote
4
replies
1.0k
views
tximport abundanceCol parameter not functioning for rsem data
tximport
rsem
transcript abundance
TPM
FPKM
updated 3.5 years ago by
Michael Love
42k • written 3.7 years ago by
m.metsger
• 0
2
votes
4
replies
1.5k
views
How to get TPM / FPKM after batch correction with DESeq2?
DESeq2
BatchEffect
tpm
fpkm
13 months ago
vk
• 0
1
vote
4
replies
4.4k
views
Conversion from FPKM,RPKM to tpm
DESEQ2
fpkm
rpkm
tpm
2.6 years ago
Sandhiya
• 0
1
vote
4
replies
1.5k
views
merge TPM values for same geneID
RNASeqRData
TPM
updated 19 months ago by
ATpoint
★ 4.1k • written 19 months ago by
prashali.bansal
▴ 10
1
vote
3
replies
4.5k
views
PCA from TPM
pca
tpm
tximport
6.6 years ago
tanyabioinfo
▴ 20
2
votes
3
replies
1.7k
views
TPM from STAR mapped counts
GeneExpression
GenomicFeatures
RNA-Seq
TPM
updated 8 months ago by
Gordon Smyth
50k • written 8 months ago by
gingergeiger22
• 0
1
vote
3
replies
1.5k
views
Selecting genes that best separate between two groups
limma
genefilter
ttest
clustering
TPM
6.7 years ago
lirongrossmann
▴ 80
2
votes
3
replies
1.4k
views
RNA-seq: Time-course data normalisation with TPM
rna-seq
normalization
deseq2
TPM
updated 6.2 years ago by
Michael Love
42k • written 6.2 years ago by
heikki.sarin
▴ 10
2
votes
3
replies
1.8k
views
Normalization for within-sample gene correlation
edgeR
Normalization
DESeq2
tpm
RNASeq
updated 3.5 years ago by
Gordon Smyth
50k • written 3.5 years ago by
tcalvo
▴ 90
2
votes
2
replies
1.6k
views
How to Analyse Datasets from GEO
geo
rnaseq
deseq2
tpm
updated 4.0 years ago by
Kevin Blighe
★ 3.9k • written 4.0 years ago by
andrej.stoll.de
▴ 10
2
votes
2
replies
2.1k
views
tximport counts versus TPM
tximport
TPM
updated 3.9 years ago by
Michael Love
42k • written 3.9 years ago by
Ina Hoeschele
▴ 620
2
votes
2
replies
1.2k
views
How to use TPM in plotMA in DESeq2
TPM
deseq2
updated 5.6 years ago by
Michael Love
42k • written 5.6 years ago by
georgewwp
• 0
2
votes
2
replies
1.0k
views
Normalizing 5' Nascent RNA-seq data to identify differentially expressed transcription start sites
DESeq2
tpm
Normalization
updated 2.8 years ago by
Michael Love
42k • written 2.8 years ago by
Carlos
• 0
0
votes
2
replies
3.1k
views
Why counts to tpm gives different values compared to tpm from kallisto?
rnaseq
counts
tpm
GenomicFeatures
kallisto
updated 3.6 years ago by
Michael Love
42k • written 3.6 years ago by
m93
• 0
0
votes
2
replies
778
views
multiple correction on mean of TPM
TPM
19 months ago
Harish.Sudarsanam
• 0
0
votes
2
replies
1.6k
views
DESeq2 Log2 fold change does not make sense given change in TPM
DESeq2
TPM
Foldchange
updated 2.1 years ago by
Michael Love
42k • written 2.1 years ago by
dadca596
• 0
0
votes
1
reply
2.4k
views
Normalize depth before calculating TPM
rna-seq
TPM
library size factor
6.5 years ago
colore
• 0
0
votes
1
reply
1.5k
views
TPM and FPKM for lncRNA
GenomicFeatures
TPM
FPKM
lncRNA
6.0 years ago
Ina Hoeschele
▴ 620
0
votes
1
reply
1.2k
views
Using TPM of a specific isoform as a phenotype for gene set enrichment analysis
deseq2
gsea
tpm
rnaseq
salmon rna seq
updated 5.6 years ago by
Michael Love
42k • written 5.6 years ago by
leo_CD
• 0
0
votes
1
reply
1.5k
views
Set rnaseq locial flag during GSVA
gsva
rnaseq
tpm
updated 6.7 years ago by
Robert Castelo
★ 3.3k • written 6.8 years ago by
leiendeckerlu
• 0
0
votes
1
reply
2.1k
views
Unsupervised heatmap use tpm or rlog gave different results
deseq2
tpm
heatmap
pheatmap
updated 6.9 years ago by
Michael Love
42k • written 6.9 years ago by
jarod_v6@libero.it
▴ 40
2
votes
1
reply
2.0k
views
ensembl to hgnc symbols creates duplicates
r
biomart
genemap
TPM
updated 3.8 years ago by
Kevin Blighe
★ 3.9k • written 3.8 years ago by
Matan G.
▴ 60
0
votes
1
reply
731
views
How to make the data compatible for DESeq2?
DESeq2
TPM
rawcounts
StringTie
updated 21 months ago by
Michael Love
42k • written 21 months ago by
snijesh
▴ 20
0
votes
0
replies
1.2k
views
ExpressionAtlas: download RPKM/TPM
ExpressionAtlas
EMBL
TPM
6.4 years ago
António Miguel de Jesus Domingues
▴ 510
33 results • Page
1 of 1
Recent ...
Replies
Answer: Numerical differences in DESeq2 output depending on different design matrix cons
by
Michael Love
42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs
by
Michael Love
42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
swbarnes2
★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Comment: DESeq2- Mysterious interaction suppresses DEGs
by
shaunpeterson
• 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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