Showing : tpm • reset
2
votes
3
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2.2k
views
TPM from STAR mapped counts
GeneExpression GenomicFeatures RNA-Seq TPM
updated 10 months ago by 51k • written 10 months ago by • 0
2
votes
4
replies
1.7k
views
How to get TPM / FPKM after batch correction with DESeq2?
DESeq2 BatchEffect tpm fpkm
15 months ago vk • 0
0
votes
2
replies
865
views
multiple correction on mean of TPM
TPM
21 months ago Harish.Sudarsanam • 0
1
vote
4
replies
1.6k
views
merge TPM values for same geneID
RNASeqRData TPM
updated 22 months ago by ★ 4.2k • written 22 months ago by ▴ 10
0
votes
1
reply
776
views
How to make the data compatible for DESeq2?
DESeq2 TPM rawcounts StringTie
updated 23 months ago by 42k • written 23 months ago by ▴ 20
4
votes
5
replies
2.4k
views
Which is the best type of data for correlation or survival analysis
TPM RNASeq RSEM DESeq2
updated 23 months ago by 42k • written 24 months ago by ▴ 10
0
votes
2
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1.7k
views
DESeq2 Log2 fold change does not make sense given change in TPM
DESeq2 TPM Foldchange
updated 2.3 years ago by 42k • written 2.3 years ago by • 0
1
vote
4
replies
4.6k
views
Conversion from FPKM,RPKM to tpm
DESEQ2 fpkm rpkm tpm
2.8 years ago Sandhiya • 0
2
votes
2
replies
1.1k
views
Normalizing 5' Nascent RNA-seq data to identify differentially expressed transcription start sites
DESeq2 tpm Normalization
updated 3.0 years ago by 42k • written 3.0 years ago by • 0
2
votes
3
replies
2.0k
views
Normalization for within-sample gene correlation
edgeR Normalization DESeq2 tpm RNASeq
updated 3.7 years ago by 51k • written 3.7 years ago by ▴ 90
1
vote
4
replies
1.1k
views
tximport abundanceCol parameter not functioning for rsem data
tximport rsem transcript abundance TPM FPKM
updated 3.7 years ago by 42k • written 3.9 years ago by • 0
0
votes
2
replies
3.3k
views
Why counts to tpm gives different values compared to tpm from kallisto?
rnaseq counts tpm GenomicFeatures kallisto
updated 3.7 years ago by 42k • written 3.7 years ago by • 0
2
votes
1
reply
2.2k
views
ensembl to hgnc symbols creates duplicates
r biomart genemap TPM
updated 4.0 years ago by ★ 4.0k • written 4.0 years ago by ▴ 60
2
votes
2
replies
2.2k
views
tximport counts versus TPM
tximport TPM
updated 4.1 years ago by 42k • written 4.1 years ago by ▴ 620
2
votes
2
replies
1.8k
views
How to Analyse Datasets from GEO
geo rnaseq deseq2 tpm
updated 4.2 years ago by ★ 4.0k • written 4.2 years ago by ▴ 10
5
votes
8
replies
1.9k
views
Unexpected results while analyzing a subset of genes in GEO RNAseq dataset containing TPM values
R limma TPM rnaseq differential expression
updated 4.8 years ago by ★ 13k • written 4.8 years ago by ▴ 30
16
votes
25
replies
3.3k
views
dtuScaledTPM vs lengthScaledTPM in DTU analysis
tximport dtu salmon TPM rnaseqDTU
written 5.3 years ago by ▴ 60
6
votes
8
replies
2.9k
views
Use of pseudoalignment estimated counts as input to edgeR and Limma-Voom
RNASeq-quantification edgeR TPM
updated 5.5 years ago by 51k • written 5.5 years ago by ▴ 20
2
votes
2
replies
1.3k
views
How to use TPM in plotMA in DESeq2
TPM deseq2
updated 5.8 years ago by 42k • written 5.8 years ago by • 0
0
votes
1
reply
1.3k
views
Using TPM of a specific isoform as a phenotype for gene set enrichment analysis
deseq2 gsea tpm rnaseq salmon rna seq
updated 5.8 years ago by 42k • written 5.8 years ago by • 0
0
votes
1
reply
1.6k
views
TPM and FPKM for lncRNA
GenomicFeatures TPM FPKM lncRNA
6.2 years ago Ina Hoeschele ▴ 620
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 6.3 years ago by ▴ 20 • written 8.0 years ago by ▴ 190
2
votes
18
replies
3.6k
views
Using tximport on rsem files produces error while trying to read in files
R tximport rnaseq tpm rsem
6.3 years ago stephan.emmrich ▴ 10
2
votes
3
replies
1.5k
views
RNA-seq: Time-course data normalisation with TPM
rna-seq normalization deseq2 TPM
updated 6.4 years ago by 42k • written 6.4 years ago by ▴ 10
0
votes
0
replies
1.2k
views
ExpressionAtlas: download RPKM/TPM
ExpressionAtlas EMBL TPM
6.6 years ago António Miguel de Jesus Domingues ▴ 510
0
votes
1
reply
2.4k
views
Normalize depth before calculating TPM
rna-seq TPM library size factor
6.7 years ago colore • 0
1
vote
3
replies
4.7k
views
PCA from TPM
pca tpm tximport
6.8 years ago tanyabioinfo ▴ 20
1
vote
3
replies
1.6k
views
Selecting genes that best separate between two groups
limma genefilter ttest clustering TPM
6.9 years ago lirongrossmann ▴ 80
0
votes
1
reply
1.6k
views
Set rnaseq locial flag during GSVA
gsva rnaseq tpm
updated 6.9 years ago by ★ 3.3k • written 7.0 years ago by • 0
2
votes
14
replies
7.9k
views
Calculating rpkm from counts data?
r featurecounts rpkm tpm edger
updated 17 months ago by ▴ 20 • written 7.0 years ago by ▴ 120
33
votes
16
replies
41k
views
Differential expression analysis starting from TPM data
R TPM
updated 7.0 years ago by 51k • written 7.0 years ago by ▴ 90
0
votes
1
reply
2.1k
views
Unsupervised heatmap use tpm or rlog gave different results
deseq2 tpm heatmap pheatmap
updated 7.1 years ago by 42k • written 7.1 years ago by ▴ 40
2
votes
5
replies
11k
views
Normalization of RNA-seq data: between samples and within samples
rnaseq normalization tpm tmm
8.8 years ago nickbern92 • 0
33 results • Page 1 of 1
Recent ...
Replies
Comment: 'path' must be string by James W. MacDonald 66k
Yes. We already knew that from the error message, and I told you that in my previous email. The point wasn't to figure out *where* the err…
Comment: 'path' must be string by cpierce2 • 0
I ran the debugger and this is the line that causes the error: ``` if (any(startsWith(pkcData[["RTS_ID"]][1L], "RTS")) & any(startsWith(pr…
Comment: Generating surrogate variables across multiple variables of interest by Robert • 0
Yes, we have several biomarkers, and a proteomic set, so we are characterizing each biomarker by it's proteomic association(s). The use for…
Comment: Error running tximeta by Guido Hooiveld ★ 4.0k
FYI (since I just finalized a run with `salmon`). For each sample (`.`) an output folder is created that contains 3 files (`cmd_info.json`…
Comment: Error running tximeta by Michael Love 42k
Tximeta uses the full directory. There are files that give the key information about the transcriptome. It's not a good idea to selectively…
Votes
Question: Deconvolution Methods on RNA-Seq Data (Mixed cell types)
Answer: Understanding how to contrast two treatments in DESeq2
Answer: Understanding how to contrast two treatments in DESeq2
Cannot extract TxFeatures for a defined GRanges object
Limma time series spline help
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