Showing : tpm • reset
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
17k
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
16
votes
25
replies
2.9k
views
dtuScaledTPM vs lengthScaledTPM in DTU analysis
tximport dtu salmon TPM rnaseqDTU
written 5.0 years ago by ▴ 60
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
5
votes
8
replies
1.7k
views
Unexpected results while analyzing a subset of genes in GEO RNAseq dataset containing TPM values
R limma TPM rnaseq differential expression
updated 4.5 years ago by ★ 13k • written 4.5 years ago by ▴ 30
4
votes
5
replies
2.1k
views
Which is the best type of data for correlation or survival analysis
TPM RNASeq RSEM DESeq2
updated 20 months ago by 41k • written 20 months ago by ▴ 10
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
2
votes
14
replies
7.5k
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
3
replies
1.4k
views
RNA-seq: Time-course data normalisation with TPM
rna-seq normalization deseq2 TPM
updated 6.1 years ago by 41k • written 6.1 years ago by ▴ 10
2
votes
18
replies
3.4k
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
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
2
replies
1.5k
views
How to Analyse Datasets from GEO
geo rnaseq deseq2 tpm
updated 3.9 years ago by ★ 3.9k • written 4.0 years ago by ▴ 10
2
votes
2
replies
2.0k
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
1.9k
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
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 3.4 years ago by ▴ 90
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
2
votes
3
replies
1.5k
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
5
replies
11k
views
Normalization of RNA-seq data: between samples and within samples
rnaseq normalization tpm tmm
8.5 years ago nickbern92 • 0
1
vote
4
replies
4.2k
views
Conversion from FPKM,RPKM to tpm
DESEQ2 fpkm rpkm tpm
2.6 years ago Sandhiya • 0
1
vote
4
replies
1.4k
views
merge TPM values for same geneID
RNASeqRData TPM
updated 18 months ago by ★ 4.0k • written 18 months ago by ▴ 10
1
vote
3
replies
4.4k
views
PCA from TPM
pca tpm tximport
6.5 years ago tanyabioinfo ▴ 20
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
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
0
votes
1
reply
704
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
0
votes
2
replies
741
views
multiple correction on mean of TPM
TPM
18 months ago Harish.Sudarsanam • 0
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
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
0
votes
1
reply
2.1k
views
Unsupervised heatmap use tpm or rlog gave different results
deseq2 tpm heatmap pheatmap
updated 6.8 years ago by 41k • written 6.8 years ago by ▴ 40
0
votes
1
reply
1.5k
views
Set rnaseq locial flag during GSVA
gsva rnaseq tpm
updated 6.6 years ago by ★ 3.2k • written 6.7 years ago by • 0
0
votes
2
replies
1.5k
views
DESeq2 Log2 fold change does not make sense given change in TPM
DESeq2 TPM Foldchange
updated 2.0 years ago by 41k • written 2.0 years ago by • 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 3.5 years ago by 41k • written 3.5 years ago by • 0
0
votes
1
reply
2.3k
views
Normalize depth before calculating TPM
rna-seq TPM library size factor
6.4 years ago colore • 0
0
votes
0
replies
1.2k
views
ExpressionAtlas: download RPKM/TPM
ExpressionAtlas EMBL TPM
6.3 years ago António Miguel de Jesus Domingues ▴ 490
33 results • Page 1 of 1
Recent ...
Replies
Comment: Differential peaks that were not identified in diffbind were identified in diseq by ATpoint ★ 4.0k
Make an MAplot. There is almost certainly an issue with normalization here given the very biased distribution of logFCs as in this Volcano.
Comment: significant difference of p-values with dream() after updating VariancePartition by gabriel.hoffman ▴ 100
See variancePartition updates for [v1.33.11](https://diseaseneurogenomics.github.io/variancePartition/news/index.html#variancepartition-133…
Comment: A ComBat-seq issue: the covariates are confounded by W. Evan Johnson ▴ 850
This is only partially confounded because there is overlap between the batches -- they both have GFP controls that can be used to remove ba…
Answer: Different number of exons in reference genome affects DEXSeq analysis by Alejandro Reyes ★ 1.9k
Likely the new annotation that you are using has more annotated isoforms, and thus the exons are splitted into more disjoint exonic bins. I…
Answer: Adding columns to DEXSeqResults object by Alejandro Reyes ★ 1.9k
I'd have a look into the match function, that could give you a mapping between the ids in the dxr1 object and your data frame of gene symbo…
Votes
Comment: DEXSeq DEXSeqDataSet count matrix duplication
Comment: Error in champ.load(): The following specified files do not exist
Answer: Error in read.metharray(basenames = files, extended = extended, verbose = verbos
Using GRanges and IRanges to simply get all chromosome data
A: Using GRanges and IRanges to simply get all chromosome data
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