Showing : txImport • reset
1
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3
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226
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miRNA differential expression analysis - treat as transcript level?
tximport DESeq2 edgeR swish miRNA
updated 3 days ago by 37k • written 8 days ago by • 0
1
vote
5
replies
109
views
RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM tximport scRNAseq DESeq2
updated 13 hours ago by 37k • written 5 days ago by • 0
0
votes
1
reply
128
views
Function Request for Rsubread or tximport: parsing command-line featureCounts output
tximport Rsubread
updated 5 weeks ago by ★ 1.3k • written 5 weeks ago by ▴ 10
0
votes
1
reply
114
views
Why TxImport Abundance is slightly different from manually added TPMs?
tximport R
updated 6 weeks ago by 37k • written 7 weeks ago by • 0
2
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3
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196
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Problem with tximport IDs
tximport tx2gene rnas DESeq2 RNASeqData
8 weeks ago Maka • 0
2
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4
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209
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confused with tximport counts abundance using salmon input
RNASeq tximport
11 weeks ago Al90 • 0
0
votes
2
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296
views
tximport ERROR : all(file.exists(files)) is not TRUE
Linux R tximport
4 months ago nakane_clan • 0
2
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5
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334
views
from kallisto to deseq2 analysis
biomaRt DESeq2 tximport
4 months ago Marianna • 0
2
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3
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261
views
Import RSEM output without sample data
DESeq2 tximportData tximport
updated 4 months ago by 37k • written 4 months ago by • 0
0
votes
1
reply
170
views
tximport
salmon tximport
updated 4 months ago by 37k • written 4 months ago by • 0
0
votes
1
reply
203
views
Ensembl dataset version
tximport rna rnaseqGene biomaRt
updated 5 months ago by ★ 1.3k • written 5 months ago by • 0
0
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3
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428
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tximport question on what counts to use for LogFC calculations
tximport
updated 7 months ago by 37k • written 7 months ago by • 0
0
votes
4
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524
views
Filtering output from tximport
tximport Salmon
updated 7 months ago by 37k • written 7 months ago by • 0
0
votes
1
reply
473
views
tximport samples with separate tx2gene maps
tximport
updated 7 months ago by 37k • written 8 months ago by • 0
1
vote
3
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641
views
tximport error: all(txId == raw[[txIdCol]]) is not TRUE
tximport
7 months ago nicolette.sipperly • 0
2
votes
1
reply
291
views
How to normalize Kallisto count matrix collapsed at gene-level with TMM/DESeq2?
DESeq2 tximport Kallisto TMM edgeR
updated 8 months ago by 37k • written 8 months ago by • 0
0
votes
2
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404
views
Error message when importing my quant.sf files into R using tximport; should I set 'ignoreTxVersion' to True or False?
Salmon ignoreTxVersion tximport
updated 10 months ago by 37k • written 10 months ago by • 0
1
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2
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323
views
tximeta countsFromAbundance for downstream analysis
tximeta tximport
10 months ago paulimer • 0
2
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3
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430
views
importing RSEM isoform to Gene Name with tximport
tximport
updated 11 months ago by 60k • written 11 months ago by ▴ 10
0
votes
3
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352
views
tximport cannot inport RSEM FPKM data
tximport
updated 7 months ago by 37k • written 2.0 years ago by • 0
1
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4
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633
views
tximport from Galaxy output
normalization tximport
updated 6 months ago by • 0 • written 3.0 years ago by ▴ 10
4
votes
3
replies
2.2k
views
tximport error: all(names(aveLengthSampGene) == rownames(lengthMat)) is not TRUE
tximport salmon R bioconductor
updated 6 months ago by • 0 • written 5.0 years ago by • 0
0
votes
7
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1.7k
views
Error reading kallisto files using tximport for cross species RNA-Seq analysis
kallisto tximport RNA-Seq across species
updated 7 months ago by • 0 • written 5.1 years ago by ▴ 40
6
votes
2
replies
5.5k
views
Using RSEM with tximport and DESeq2
deseq2 tximport software error bug
updated 9 months ago by 37k • written 5.4 years ago by • 0
24 results • Page 1 of 1
Recent ...
Replies
Answer: Analyzing barcode sequencing experiments with DESeq2/edgeR by Gordon Smyth 45k
Dai Z, Sheridan JM, Gearing, LJ, Moore, DL, Su, S, Wormald, S, Wilcox, S, O'Connor, L, Dickins, RA, Blewitt, ME, Ritchie, ME (2014). edgeR:…
Comment: How can i fix this problem in R by Habib • 0
i have input this BiocManager::install("S4Vectors") and my answer was: Error: unexpected '&' in "BiocManager::install(&"
Answer: How can i fix this problem in R by Steve Lianoglou 13k
This could be a sign of a b0rked installation, but I'd start with trying to reinstall the S4Vectors package and seeing what new issues (if …
Comment: Using Age or other numerical variable to model expression in deseq2 by krushnach80 • 0
yes in my metadata I checked its not turned into factor.. simple question what is the `intercept` in case of when I using age in my design …
Comment: Use of Scater for QC in scRNA-seq: How to remove cells with less than certain nu by ATpoint ★ 1.3k
x-posted: https://www.biostars.org/p/9528980/
Votes
Comment: Using Age or other numerical variable to model expression in deseq2
Comment: Using Age or other numerical variable to model expression in deseq2
C: DESeq2 lfcShrink() usage of coef vs. usage of contrast
C: DESeq2 lfcShrink() usage of coef vs. usage of contrast
Comment: Using Age or other numerical variable to model expression in deseq2
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