Showing : TPM • reset
2
votes
3
replies
227
views
TPM from STAR mapped counts
GeneExpression GenomicFeatures RNA-Seq TPM
updated 11 days ago by 48k • written 14 days ago by • 0
2
votes
4
replies
617
views
How to get TPM / FPKM after batch correction with DESeq2?
DESeq2 BatchEffect tpm fpkm
5 months ago vk • 0
0
votes
2
replies
503
views
multiple correction on mean of TPM
TPM
11 months ago Harish.Sudarsanam • 0
1
vote
4
replies
910
views
merge TPM values for same geneID
RNASeqRData TPM
updated 12 months ago by ★ 3.4k • written 12 months ago by ▴ 10
0
votes
1
reply
504
views
How to make the data compatible for DESeq2?
DESeq2 TPM rawcounts StringTie
updated 13 months ago by 40k • written 13 months ago by ▴ 20
4
votes
5
replies
1.4k
views
Which is the best type of data for correlation or survival analysis
TPM RNASeq RSEM DESeq2
updated 13 months ago by 40k • written 13 months ago by ▴ 10
0
votes
2
replies
1.2k
views
DESeq2 Log2 fold change does not make sense given change in TPM
DESeq2 TPM Foldchange
updated 18 months ago by 40k • written 18 months ago by • 0
1
vote
4
replies
3.5k
views
Conversion from FPKM,RPKM to tpm
DESEQ2 fpkm rpkm tpm
2.0 years ago Sandhiya • 0
2
votes
2
replies
800
views
Normalizing 5' Nascent RNA-seq data to identify differentially expressed transcription start sites
DESeq2 tpm Normalization
updated 2.1 years ago by 40k • written 2.1 years ago by • 0
2
votes
3
replies
1.3k
views
Normalization for within-sample gene correlation
edgeR Normalization DESeq2 tpm RNASeq
updated 2.9 years ago by 48k • written 2.9 years ago by ▴ 90
1
vote
4
replies
803
views
tximport abundanceCol parameter not functioning for rsem data
tximport rsem transcript abundance TPM FPKM
updated 2.9 years ago by 40k • written 3.0 years ago by • 0
0
votes
2
replies
2.5k
views
Why counts to tpm gives different values compared to tpm from kallisto?
rnaseq counts tpm GenomicFeatures kallisto
updated 2.9 years ago by 40k • written 2.9 years ago by • 0
1
vote
1
reply
1.5k
views
ensembl to hgnc symbols creates duplicates
r biomart genemap TPM
updated 3.1 years ago by 3.8k • written 3.1 years ago by ▴ 50
2
votes
2
replies
1.6k
views
tximport counts versus TPM
tximport TPM
updated 3.2 years ago by 40k • written 3.2 years ago by ▴ 620
2
votes
2
replies
1.2k
views
How to Analyse Datasets from GEO
geo rnaseq deseq2 tpm
updated 3.4 years ago by 3.8k • written 3.4 years ago by ▴ 10
5
votes
8
replies
1.3k
views
Unexpected results while analyzing a subset of genes in GEO RNAseq dataset containing TPM values
R limma TPM rnaseq differential expression
updated 4.0 years ago by 13k • written 4.0 years ago by ▴ 30
14
votes
25
replies
2.2k
views
dtuScaledTPM vs lengthScaledTPM in DTU analysis
tximport dtu salmon TPM rnaseqDTU
written 4.5 years ago by ▴ 60
6
votes
8
replies
2.3k
views
Use of pseudoalignment estimated counts as input to edgeR and Limma-Voom
RNASeq-quantification edgeR TPM
updated 4.6 years ago by 48k • written 4.6 years ago by ▴ 20
2
votes
2
replies
951
views
How to use TPM in plotMA in DESeq2
TPM deseq2
updated 4.9 years ago by 40k • written 4.9 years ago by • 0
0
votes
1
reply
996
views
Using TPM of a specific isoform as a phenotype for gene set enrichment analysis
deseq2 gsea tpm rnaseq salmon rna seq
updated 4.9 years ago by 40k • written 4.9 years ago by • 0
0
votes
1
reply
1.3k
views
TPM and FPKM for lncRNA
GenomicFeatures TPM FPKM lncRNA
5.3 years ago Ina Hoeschele ▴ 620
32
votes
16
replies
16k
views
difference among tximport scaledTPM, lengthScaledTPM and the original TPM output by salmon/kallisto
tximport deseq2 TPM RPKM rnaseq
updated 5.4 years ago by ▴ 20 • written 7.2 years ago by ▴ 190
2
votes
18
replies
3.0k
views
Using tximport on rsem files produces error while trying to read in files
R tximport rnaseq tpm rsem
5.5 years ago stephan.emmrich ▴ 10
2
votes
3
replies
1.1k
views
RNA-seq: Time-course data normalisation with TPM
rna-seq normalization deseq2 TPM
updated 5.6 years ago by 40k • written 5.6 years ago by ▴ 10
0
votes
0
replies
920
views
ExpressionAtlas: download RPKM/TPM
ExpressionAtlas EMBL TPM
5.8 years ago António Miguel de Jesus Domingues ▴ 490
0
votes
1
reply
2.0k
views
Normalize depth before calculating TPM
rna-seq TPM library size factor
5.9 years ago colore • 0
1
vote
3
replies
3.9k
views
PCA from TPM
pca tpm tximport
5.9 years ago tanyabioinfo ▴ 20
1
vote
3
replies
1.2k
views
Selecting genes that best separate between two groups
limma genefilter ttest clustering TPM
6.0 years ago lirongrossmann ▴ 80
0
votes
1
reply
1.3k
views
Set rnaseq locial flag during GSVA
gsva rnaseq tpm
updated 6.1 years ago by ★ 3.0k • written 6.1 years ago by • 0
2
votes
14
replies
6.6k
views
Calculating rpkm from counts data?
r featurecounts rpkm tpm edger
updated 7 months ago by • 0 • written 6.1 years ago by ▴ 110
33
votes
16
replies
35k
views
Differential expression analysis starting from TPM data
R TPM
updated 6.2 years ago by 48k • written 6.2 years ago by ▴ 90
0
votes
1
reply
1.9k
views
Unsupervised heatmap use tpm or rlog gave different results
deseq2 tpm heatmap pheatmap
updated 6.3 years ago by 40k • written 6.3 years ago by ▴ 40
2
votes
5
replies
10k
views
Normalization of RNA-seq data: between samples and within samples
rnaseq normalization tpm tmm
8.0 years ago nickbern92 • 0
33 results • Page 1 of 1
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Replies
Comment: DiffBind handling of replicates and consensus by Rory Stark ★ 5.0k
You may want to try different values for the `normalize` parameter: dbObj <- dba.normalize(DBA = dbObj, library = "RiP", normalize=DBA…
Comment: DiffBind: dba.plotProfile(profiles) by Rory Stark ★ 5.0k
Yes, setting `raster_quality` down is a good way to address this issue. I've taken to using `raster_quality=1` in general as I think the pl…
Comment: DiffBind: dba.plotProfile(profiles) by Dorien ▴ 10
Not really an answer as I don't know really know why , but I also had the same issue and may have found a workaround ! If I set maxSites > …
Comment: Suggested package missing from Development version of Bioconductor by shepherl 3.5k
Is your package in review or already in Bioconductor? Its harder if it is in review because we can't tell that the package has or can build…
Comment: biomaRt code/getBM function no longer importing 'coding' sequence via seqType ar by andrew.b.kleist • 0
This worked perfectly! I was able to retrieve the sequences of interest using ```host="https://grch37.ensembl.org"``` within the useEnsembl…
Votes
Answer: DiffBind - how to prep the sample matrix when multiple bam files are used by MAC
Comment: DiffBind: dba.plotProfile(profiles)
Normalisation of data using DESeq2 with multi-groups
Answer: Normalisation of data using DESeq2 with multi-groups
Answer: Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
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