Showing : TPM • reset
2
votes
3
replies
1.6k
views
TPM from STAR mapped counts
GeneExpression GenomicFeatures RNA-Seq TPM
updated 7 months ago by 50k • written 7 months ago by • 0
2
votes
14
replies
7.6k
views
Calculating rpkm from counts data?
r featurecounts rpkm tpm edger
updated 14 months ago by • 0 • written 6.7 years ago by ▴ 110
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
6
votes
8
replies
2.7k
views
Use of pseudoalignment estimated counts as input to edgeR and Limma-Voom
RNASeq-quantification edgeR TPM
updated 5.2 years ago by 50k • written 5.2 years ago by ▴ 20
33
votes
16
replies
39k
views
Differential expression analysis starting from TPM data
R TPM
updated 6.7 years ago by 50k • written 6.7 years ago by ▴ 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 6.0 years ago by ▴ 20 • written 7.8 years ago by ▴ 190
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
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 5.5 years ago by 41k • written 5.5 years ago by • 0
2
votes
2
replies
1.2k
views
How to use TPM in plotMA in DESeq2
TPM deseq2
updated 5.5 years ago by 41k • written 5.5 years ago by • 0
2
votes
4
replies
1.4k
views
How to get TPM / FPKM after batch correction with DESeq2?
DESeq2 BatchEffect tpm fpkm
12 months ago vk • 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 41k • written 6.9 years ago by ▴ 40
0
votes
1
reply
1.5k
views
Set rnaseq locial flag during GSVA
gsva rnaseq tpm
updated 6.7 years ago by ★ 3.3k • written 6.7 years ago by • 0
1
vote
3
replies
4.5k
views
PCA from TPM
pca tpm tximport
6.5 years ago tanyabioinfo ▴ 20
0
votes
1
reply
2.3k
views
Normalize depth before calculating TPM
rna-seq TPM library size factor
6.4 years ago colore • 0
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 41k • written 6.2 years ago by ▴ 10
2
votes
2
replies
1.0k
views
Normalizing 5' Nascent RNA-seq data to identify differentially expressed transcription start sites
DESeq2 tpm Normalization
updated 2.7 years ago by 41k • written 2.7 years ago by • 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 41k • written 2.1 years ago by • 0
0
votes
1
reply
725
views
How to make the data compatible for DESeq2?
DESeq2 TPM rawcounts StringTie
updated 20 months ago by 41k • written 20 months ago by ▴ 20
4
votes
5
replies
2.2k
views
Which is the best type of data for correlation or survival analysis
TPM RNASeq RSEM DESeq2
updated 20 months ago by 41k • written 21 months ago by ▴ 10
1
vote
4
replies
4.3k
views
Conversion from FPKM,RPKM to tpm
DESEQ2 fpkm rpkm tpm
2.6 years ago Sandhiya • 0
16
votes
25
replies
3.0k
views
dtuScaledTPM vs lengthScaledTPM in DTU analysis
tximport dtu salmon TPM rnaseqDTU
written 5.1 years ago by ▴ 60
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 ★ 13k • written 4.6 years ago by ▴ 30
2
votes
2
replies
1.5k
views
How to Analyse Datasets from GEO
geo rnaseq deseq2 tpm
updated 4.0 years ago by ★ 3.9k • written 4.0 years ago by ▴ 10
2
votes
2
replies
2.1k
views
tximport counts versus TPM
tximport TPM
updated 3.8 years ago by 41k • written 3.8 years ago by ▴ 620
2
votes
1
reply
2.0k
views
ensembl to hgnc symbols creates duplicates
r biomart genemap TPM
updated 3.7 years ago by ★ 3.9k • written 3.7 years ago by ▴ 60
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 41k • written 3.6 years ago by • 0
2
votes
3
replies
1.7k
views
Normalization for within-sample gene correlation
edgeR Normalization DESeq2 tpm RNASeq
updated 3.4 years ago by 50k • written 3.5 years ago by ▴ 90
1
vote
4
replies
1.4k
views
merge TPM values for same geneID
RNASeqRData TPM
updated 19 months ago by ★ 4.1k • written 19 months ago by ▴ 10
0
votes
1
reply
1.5k
views
TPM and FPKM for lncRNA
GenomicFeatures TPM FPKM lncRNA
5.9 years ago Ina Hoeschele ▴ 620
0
votes
2
replies
754
views
multiple correction on mean of TPM
TPM
18 months ago Harish.Sudarsanam • 0
0
votes
0
replies
1.2k
views
ExpressionAtlas: download RPKM/TPM
ExpressionAtlas EMBL TPM
6.4 years ago António Miguel de Jesus Domingues ▴ 510
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 3.5 years ago by 41k • written 3.5 years ago by • 0
1
vote
3
replies
1.5k
views
Selecting genes that best separate between two groups
limma genefilter ttest clustering TPM
6.6 years ago lirongrossmann ▴ 80
33 results • Page 1 of 1
Recent ...
Replies
Comment: limma-voom: Calculate the log-fold change in gene expression within a sample by xofer16091 • 0
A few more names for [dino game][1] are Dino Dun, Chrome Dino, T-Rex, Google, and No Internet games. You can play the online game on a tabl…
Comment: Differences in differential analysis methods for RNA-Seq by ATpoint ★ 4.1k
MAGeCK is a command line tool that is easy to use. I recommend you use it because a) the logFCs from DESeq2 and MAGeCK will be very similar…
Comment: Get genomic coordinates of CpGs sites (chromosomes, genomic position) by Yveto • 0
Thank for your response. It is Illumina 450 K. I use this code ```{r } library(IlluminaHumanMethylation450kanno.ilmn12.hg19) annotat…
Answer: More regions in union when increasing DBA$config$mergeOverlap by Rory Stark ★ 5.2k
I think the documentation is out of sync with the code. Positive values represent gaps between intervals and negative values represent how …
Comment: log2FoldChange value is way too different when compared with counts(dds) by Michael Love 41k
But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…
Votes
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
SPIA plotP giving error
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