Showing : txImport • reset
2
votes
8
replies
335
views
RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM tximport scRNAseq DESeq2
7 weeks ago • updated 5 weeks ago Kelen • 0
0
votes
7
replies
1.7k
views
Error reading kallisto files using tximport for cross species RNA-Seq analysis
kallisto tximport RNA-Seq across species
updated 9 months ago by • 0 • written 5.2 years ago by ▴ 40
2
votes
5
replies
411
views
from kallisto to deseq2 analysis
biomaRt DESeq2 tximport
5 months ago Marianna • 0
0
votes
4
replies
151
views
Alternative for wininet method in tximeta
DESeq2 tximport tximportData tximeta
6 weeks ago uhlkatie • 0
1
vote
4
replies
664
views
tximport from Galaxy output
normalization tximport
updated 8 months ago by • 0 • written 3.1 years ago by ▴ 10
2
votes
4
replies
270
views
confused with tximport counts abundance using salmon input
RNASeq tximport
4 months ago Al90 • 0
0
votes
4
replies
575
views
Filtering output from tximport
tximport Salmon
updated 8 months ago by 37k • written 8 months ago by • 0
4
votes
3
replies
2.2k
views
tximport error: all(names(aveLengthSampGene) == rownames(lengthMat)) is not TRUE
tximport salmon R bioconductor
updated 7 months ago by • 0 • written 5.1 years ago by • 0
0
votes
3
replies
363
views
tximport cannot inport RSEM FPKM data
tximport
updated 9 months ago by 37k • written 2.1 years ago by • 0
0
votes
3
replies
471
views
tximport question on what counts to use for LogFC calculations
tximport
updated 8 months ago by 37k • written 8 months ago by • 0
2
votes
3
replies
265
views
Problem with tximport IDs
tximport tx2gene rnas DESeq2 RNASeqData
3 months ago Maka • 0
2
votes
3
replies
297
views
Import RSEM output without sample data
DESeq2 tximportData tximport
updated 5 months ago by 37k • written 6 months ago by • 0
1
vote
3
replies
333
views
miRNA differential expression analysis - treat as transcript level?
tximport DESeq2 edgeR swish miRNA
updated 6 weeks ago by 37k • written 7 weeks ago by • 0
1
vote
3
replies
747
views
tximport error: all(txId == raw[[txIdCol]]) is not TRUE
tximport
9 months ago nicolette.sipperly • 0
0
votes
2
replies
401
views
tximport ERROR : all(file.exists(files)) is not TRUE
Linux R tximport
5 months ago nakane_clan • 0
0
votes
2
replies
475
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 11 months ago by 37k • written 11 months ago by • 0
6
votes
2
replies
5.7k
views
Using RSEM with tximport and DESeq2
deseq2 tximport software error bug
updated 11 months ago by 37k • written 5.5 years ago by • 0
0
votes
1
reply
202
views
tximport
salmon tximport
updated 6 months ago by 37k • written 6 months ago by • 0
0
votes
1
reply
506
views
tximport samples with separate tx2gene maps
tximport
updated 9 months ago by 37k • written 10 months ago by • 0
0
votes
1
reply
155
views
Why TxImport Abundance is slightly different from manually added TPMs?
tximport R
updated 3 months ago by 37k • written 3 months ago by • 0
0
votes
1
reply
162
views
Function Request for Rsubread or tximport: parsing command-line featureCounts output
tximport Rsubread
updated 12 weeks ago by ★ 1.4k • written 12 weeks ago by ▴ 10
0
votes
1
reply
246
views
Ensembl dataset version
tximport rna rnaseqGene biomaRt
updated 7 months ago by ★ 1.4k • written 7 months ago by • 0
2
votes
1
reply
363
views
How to normalize Kallisto count matrix collapsed at gene-level with TMM/DESeq2?
DESeq2 tximport Kallisto TMM edgeR
updated 10 months ago by 37k • written 10 months ago by • 0
23 results • Page 1 of 1
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Replies
Comment: IsoformSwitchAnalyzeR package on mouse data by bpshtiwan ▴ 10
Hello Ryan, Also, I am not able to find esemble file that has haplotype info in it. Kindly, have you solved the problem? Best
Comment: Design and contrast matrices for analyzing the effect of two factors of interest by Gordon Smyth 46k
I understand that your mock dataset has expression data for just one protein instead of 8000, but is the phenoData complete? Does your real…
Comment: error running UniProt.ws by James W. MacDonald 60k
Or maybe it is a quick fix! Nicely done Marcel!
Answer: Error with TCGA package - TCGAbiolinks by Tiago C. Silva ▴ 220
It is working with the github version. Could you update please? BiocManager::install("BioinformaticsFMRP/TCGAbiolinksGUI.data") …
Comment: Error with TCGA package - TCGAbiolinks by Marcel Ramos 570
You can try the Genomic Data Commons Data Portal at [https://portal.gdc.cancer.gov/][1] or the `GenomicDataCommons` R/Bioconductor packag…
Votes
A: Importance of Order in Design Formula
remove microarray batch effects using Limma
On empirical Bayes of edgeR
Answer: CQN to DESeq2
Comment: package 'BiocInstaller' is not available (for R version 3.4.4)
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