Showing : txImportData • reset
0
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4
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521
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Create count matrix from multible quant sf files from different directories
tximportData tximport salmon
4 months ago JG13 • 0
2
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9
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1.6k
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Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport tximportData DESeq2
15 months ago Ndimensional ▴ 20
0
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2
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871
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tximport error in reading salmon output files?
tximport tximportData
updated 8 months ago by • 0 • written 16 months ago by • 0
2
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3
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1.6k
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Error while reading rsem files in tximport
DESeq2 tximport rsem RNASeq tximportData
22 months ago mohammedtoufiq91 ▴ 10
3
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3
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1.3k
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What is the correct way to import transcript abundances from 3' Quantseq results that calculated by kallisto?
tximport tximportData Quantseq kallisto
24 months ago • updated 23 months ago duhwa.lee • 0
0
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4
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1.4k
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Alternative for wininet method in tximeta
DESeq2 tximport tximportData tximeta
2.3 years ago uhlkatie • 0
2
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3
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1.1k
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Import RSEM output without sample data
DESeq2 tximportData tximport
updated 2.7 years ago by 42k • written 2.7 years ago by • 0
0
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3
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1.1k
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tximport fails when RSEM output options produce files with additional columns?
DESeq2 tximportData tximpor
updated 3.2 years ago by 42k • written 3.3 years ago by • 0
0
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1
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977
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Multi-factor Analysis in DeSEQ2
tximport R tximportData RNASeq DESeq2
updated 3.4 years ago by 42k • written 3.4 years ago by • 0
0
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7
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1.9k
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Problem with Tximport
tximportData tximport
3.7 years ago agoesmartini • 0
0
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1
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1.0k
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How to use tx import on output of abundance file
tximportData tximport
updated 3.9 years ago by ★ 4.0k • written 3.9 years ago by • 0
0
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4
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1.4k
views
Having a hard time creating a Txi object from an existing Salmon output file to convert transcript file to gene id TPM
Salmon tximport tximportdata ensembl
updated 4.5 years ago by 42k • written 4.5 years ago by • 0
1
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2
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1.2k
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What is the expected location of bootstrap samples relative to quant.sf file ?
tximport tximportdata salmon
6.0 years ago fcuy047 • 0
1
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2
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1.3k
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trouble importing data for DEseq2 workflow
deseq2 tximport tximportdata pasilla Tutorial
updated 6.0 years ago by 42k • written 6.0 years ago by • 0
1
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8
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35k
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How to create tx2gene.gencode.v27.csv
tximportdata
updated 6.3 years ago by 42k • written 6.3 years ago by • 0
2
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6
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1.8k
views
[DESeq2] Different results from tutorial
deseq2 tximportdata tximport
updated 6.4 years ago by 42k • written 6.4 years ago by • 0
0
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1
reply
2.6k
views
could not find function "tximport"
tximportdata
updated 6.6 years ago by 51k • written 6.6 years ago by ▴ 30
0
votes
9
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3.7k
views
Upgrade bioconductor 3.2 to 3.3
bioclIte tximportData
updated 6.7 years ago by ▴ 80 • written 8.3 years ago by ▴ 40
0
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3
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14k
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Problem installing tximportData
tximportdata
7.6 years ago elg • 0
3
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5
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2.9k
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txImport: a gene seems missing from the sample data
txImportData txImport
updated 3.7 years ago by 67k • written 7.6 years ago by • 0
0
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1
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1.8k
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How to remove genes with 0 counts in tximport?
tximport deseq tximportdata deseq2
updated 7.7 years ago by 42k • written 7.7 years ago by ▴ 10
0
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7
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1.9k
views
PCA results different from th same sample but different counting method
deseq2 pca tximportdata htseqcounts
updated 8.3 years ago by 42k • written 8.3 years ago by ▴ 40
22 results • Page 1 of 1
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Answer: Need help interpreting heatmaps from limma by James W. MacDonald 67k
Heatmaps don't do any comparisons. They just plot the underlying data in a matrix and color the blocks based (in your case) on the by-gene …
Comment: Are transformed values from rlog /vst log2 normalized counts? by Eva ▴ 10
I understood exactly what you said, but I got confused with the documentation and the info that gives about rlog because it seems to be tha…
Answer: featureCounts fails to load annotation file by James W. MacDonald 67k
I imagine Wei Shi will be along later with actual help, but for now do note that you can use an SAF file instead of a GTF. It's easy enough…
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function by James W. MacDonald 67k
That error indicates that you have a file called NCBI.sqlite in your working directory that is missing some tables. You should delete that …
Comment: Are transformed values from rlog /vst log2 normalized counts? by James W. MacDonald 67k
The `DESeq2` package is meant to analyze count data! Most packages that are intended to be used for RNA-Seq data are going to want the raw …
Votes
Answer: Are transformed values from rlog /vst log2 normalized counts?
Answer: Are transformed values from rlog /vst log2 normalized counts?
Comment: Are transformed values from rlog /vst log2 normalized counts?
Answer: Unable to install any Bioconductor package with new R 4.4.1 - path nor writable
Removing Effect of Covariate in Only a Subset of Samples in a Model Containing All Samples Loses Full Rank if Factor but not Numerical
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