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4
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3
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135
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5 follow
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Why you shouldn't normalize count data using gene-length AND library size for count analysis?
normalization metagenomics deseq2 tpm counts written 13 days ago by sundaresan.vinaik • 10
10
votes
2
answers
3.6k
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9 follow
2
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TMM or TPM normalized counts for visualization?
normalization tpm edger tmm written 17 months ago by sam.vanc70 • 30 • updated 23 days ago by simplitia • 30
2
votes
2
answers
138
views
2
answers
Using FPKM and TPM values for batch correction for Single Cell RNA-Seq
scrna-seq batch correction fpkm tpm rna-seq written 6 weeks ago by hkarakurt • 80 • updated 6 weeks ago by shoujun.gu • 250
1
vote
1
answer
474
views
1
answer
Generate gene level TPM from quant.sf file generated in salmon
R txtimport salmon rna-seq tpm written 10 weeks ago by pyrhana25 • 0 • updated 10 weeks ago by i.sudbery ♦ 6.3k
2
votes
1
answer
377
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5 follow
1
answer
How to normalized TPM with TMM method?
tpm rna-seq edger tmm written 4 months ago by xiaoguang • 10 • updated 3 months ago by Gordon Smyth • 1.1k
0
votes
0
answers
237
views
0
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TPM on SingleCell RNASeq
tpm rna-seq scrnaseq written 3 months ago by difraiadomenico • 0
8
votes
1
answer
309
views
1
answer
Metric to use for RNAseq expression matrix
expression tpm counts rna-seq batch effect written 3 months ago by RamRS ♦ 24k • updated 3 months ago by i.sudbery ♦ 6.3k
0
votes
3
answers
311
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5 follow
3
answers
Can I compare TPM values for a transcript across different transcriptome assemblies?
gene expression tpm rna-seq transcript written 3 months ago by molly77 • 10
0
votes
1
answer
162
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1
answer
HISAT2/stringtie: intron impact on expression
tpm stringtie mrna expression rna-seq hisat2 written 3 months ago by Adrian Pelin • 2.3k • updated 3 months ago by kristoffer.vittingseerup • 2.6k
2
votes
1
answer
280
views
1
answer
How to convert Xena Browser normalized RSEM values to TPM values?
xenabrowser tpm rna-seq written 5 months ago by carlee.bettler • 10 • updated 5 months ago by Charles Warden ♦ 7.3k
0
votes
0
answers
578
views
0
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Calculating FPKM and TPM by hand from htseq-count output?
htseq fpkm tpm rna-seq written 7 months ago by Joel Wallenius • 70 • updated 5 months ago by Biostar ♦♦ 20
0
votes
1
answer
271
views
1
answer
Ensembl ID and counts to FPKM/TPM
R fpkm exon tpm rna-seq written 5 months ago by jordan.mandel • 0 • updated 5 months ago by h.mon ♦ 28k
5
votes
1
answer
638
views
1
answer
How to filter low expressed genes based on TPM expression?
gene R tpm rna-seq filtering written 6 months ago by newbie • 70 • updated 6 months ago by Prakash • 1.7k
3
votes
1
answer
237
views
1
answer
problem for 2 different normalization methods in train and test data set
fpkm-uq tpm rna-seq written 8 months ago by modarzi • 90 • updated 8 months ago by Charles Warden ♦ 7.3k
2
votes
2
answers
548
views
2
answers
TPM and TMM, which should I use for clustering?
tpm clustering tmm written 8 months ago by demoraesdiogo2017 • 10 • updated 8 months ago by Charles Warden ♦ 7.3k
0
votes
0
answers
349
views
0
answers
TMM to TPM conversion
tpm tmm written 8 months ago by demoraesdiogo2017 • 10
7
votes
3
answers
1.9k
views
5 follow
3
answers
Converting TPM to FPKM
fpkm tpm rna-seq written 2.5 years ago by alexahes • 10 • updated 9 months ago by Charles Warden ♦ 7.3k
0
votes
0
answers
247
views
0
answers
Pseudotime on scRNAseq TPMs?
tpm pseudotime scrnaseq written 9 months ago by m.fletcher • 20
1
vote
0
answers
1.5k
views
0
answers
TCGA expression data (TPM)
tcgabiolinks tcga tpm expression written 15 months ago by Folder40g • 120 • updated 9 months ago by Israel Barrantes • 750
0
votes
0
answers
630
views
0
answers
Comparing gene expression of specific genes between samples in DESeq2 / R
deseq2 tpm rna-seq written 11 months ago by masicioglu • 0
0
votes
0
answers
1.7k
views
0
answers
Transforming RNA-seq data- (tpms) - what is the best practice for dealing with zeros for the purpose of deconvolution?
deconvolution cibersort tpm rna-seq written 11 months ago by nancy • 70
2
votes
1
answer
984
views
1
answer
Featurecounts normalize by gene length
featurecount deseq2 tpm written 11 months ago by David • 160
6
votes
3
answers
613
views
3
answers
DE Analysis starting from TPM matrix? Also, no replicates.
tpm rna-seq written 12 months ago by basch • 0 • updated 12 months ago by Michael Dondrup ♦ 46k
1
vote
2
answers
1.7k
views
2
answers
TMM.normalized.FPKM vs .TMM.EXPR.matrix for populating SQL
trinity fpkm tpm sql edger written 3.1 years ago by ando.kelli • 40 • updated 13 months ago by egtabilin • 0
9
votes
1
answer
826
views
6 follow
1
answer
Is it possible to make a PCA plot for samples using TPM exprssion values in R?
pca tpm rna-seq written 14 months ago by rimgubaev • 140 • updated 14 months ago by andrew.j.skelton73 ♦ 5.8k
2
votes
2
answers
2.6k
views
2
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RPKM to TPM conversion?
rpkm tpm conversion rna-seq rna written 17 months ago by brieannsobieski • 0
1
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0
answers
1.5k
views
0
answers
Kallisto TPM values
tpm kallisto written 17 months ago by oliveira.bhn • 10
5
votes
2
answers
811
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2
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How to analyse RNA-Seq data with JUST geneID and TPM values
geneid tpm rna-seq dge written 18 months ago by andorjkiss • 10 • updated 18 months ago by igor ♦ 8.8k
1
vote
1
answer
956
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1
answer
Conversion read counts to TPM for microRNAs
tpm mirna written 19 months ago by lessismore • 710 • updated 19 months ago by Buffo • 1.7k
4
votes
1
answer
4.0k
views
5 follow
1
answer
Calculating TPM Values
tpm rna-seq sequencing written 19 months ago by biocool2018 • 20 • updated 19 months ago by Tao • 350
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