Showing : tximportData • reset
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Error: lexical error: invalid char in json text (alevin-seurat)
tximpo tximportData alevinQC
updated 27 days ago by ★ 4.7k • written 4 weeks ago by • 0
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373
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Need new version : tx2gene.gencode.v47.csv
tximportData
updated 12 weeks ago by ★ 4.1k • written 12 weeks ago by • 0
4
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5
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814
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DESeq Input from Salmon + tximport/tximeta
tximportData summarizeToGene tximport DESeq2 salmon
4 months ago LuciaNhu • 0
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4
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696
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Create count matrix from multible quant sf files from different directories
tximportData tximport salmon
9 months ago JG13 • 0
2
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9
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1.9k
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Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport tximportData DESeq2
20 months ago Ndimensional ▴ 20
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1.0k
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tximport error in reading salmon output files?
tximport tximportData
updated 13 months ago by • 0 • written 21 months ago by • 0
2
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3
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1.8k
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Error while reading rsem files in tximport
DESeq2 tximport rsem RNASeq tximportData
2.3 years ago mohammedtoufiq91 ▴ 10
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3
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1.5k
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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
2.4 years ago • updated 2.3 years ago duhwa.lee • 0
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4
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1.6k
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Alternative for wininet method in tximeta
DESeq2 tximport tximportData tximeta
2.7 years ago uhlkatie • 0
2
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3
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1.3k
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Import RSEM output without sample data
DESeq2 tximportData tximport
updated 3.1 years ago by 43k • written 3.1 years ago by • 0
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1.2k
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tximport fails when RSEM output options produce files with additional columns?
DESeq2 tximportData tximpor
updated 3.7 years ago by 43k • written 3.7 years ago by • 0
0
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1.1k
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Multi-factor Analysis in DeSEQ2
tximport R tximportData RNASeq DESeq2
updated 3.8 years ago by 43k • written 3.8 years ago by • 0
0
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7
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2.1k
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Problem with Tximport
tximportData tximport
4.1 years ago agoesmartini • 0
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1
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1.2k
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How to use tx import on output of abundance file
tximportData tximport
updated 4.3 years ago by ★ 4.0k • written 4.3 years ago by • 0
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4
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1.5k
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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 4.9 years ago by 43k • written 4.9 years ago by • 0
1
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What is the expected location of bootstrap samples relative to quant.sf file ?
tximport tximportdata salmon
6.4 years ago fcuy047 • 0
1
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2
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1.4k
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trouble importing data for DEseq2 workflow
deseq2 tximport tximportdata pasilla Tutorial
updated 6.4 years ago by 43k • written 6.4 years ago by • 0
1
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8
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36k
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How to create tx2gene.gencode.v27.csv
tximportdata
updated 6.7 years ago by 43k • written 6.7 years ago by • 0
2
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6
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2.0k
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[DESeq2] Different results from tutorial
deseq2 tximportdata tximport
updated 6.8 years ago by 43k • written 6.8 years ago by • 0
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1
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2.8k
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could not find function "tximport"
tximportdata
updated 7.0 years ago by 52k • written 7.0 years ago by ▴ 30
0
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9
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3.9k
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Upgrade bioconductor 3.2 to 3.3
bioclIte tximportData
updated 7.1 years ago by ▴ 80 • written 8.7 years ago by ▴ 40
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3
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15k
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Problem installing tximportData
tximportdata
8.0 years ago elg • 0
3
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5
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3.0k
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txImport: a gene seems missing from the sample data
txImportData txImport
updated 4.1 years ago by 68k • written 8.0 years ago by • 0
1
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1
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2.0k
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How to remove genes with 0 counts in tximport?
tximport deseq tximportdata deseq2
updated 8.1 years ago by 43k • written 8.1 years ago by ▴ 20
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7
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2.0k
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PCA results different from th same sample but different counting method
deseq2 pca tximportdata htseqcounts
updated 8.7 years ago by 43k • written 8.7 years ago by ▴ 40
25 results • Page 1 of 1
Recent ...
Replies
Answer: Using tximport for kallisto aligned TOIL data by James W. MacDonald 68k
If you just have the transcript data, you probably don't need (and maybe cannot use) `tximport`. Instead you could just do the naive thing …
Answer: Reading gene expression data in GPR format and converting it to xlsx format by James W. MacDonald 68k
Setting aside the inadvisability of putting these data into Excel (and I should point out that these data are not single-cell, but instead …
Comment: concentration tables suitable as input for new packages? by wilkinson • 0
I am grateful for your response. Software such as "Spectra" may parse MS-data to generate tables of concentrations, for instance. But inste…
Comment: Removing UTR from GTF for gene quantification by ATpoint ★ 4.7k
Consider asking at biostars or bioinformatics reddit, since this is not directly related to a Bioconductor problem. Anyway, a couple of th…
Comment: Combining RNAseq and microarray data using edgeR/limma-voom by Hoover • 0
I got it! ([Drift Boss][1]) [1]: https://driftbossgame.co
Votes
Answer: Differential expression of proteins using somascan data
Answer: Surprising behavior for DEXseq dispersion estimate plot?
Answer: Handle zero effective gene length when tximport RSEM results
Handle zero effective gene length when tximport RSEM results
How to remove genes with 0 counts in tximport?
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