Showing : tximportData • reset
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Error: lexical error: invalid char in json text (alevin-seurat)
tximpo tximportData alevinQC
updated 20 days ago by ★ 4.7k • written 24 days ago by • 0
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353
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Need new version : tx2gene.gencode.v47.csv
tximportData
updated 11 weeks ago by ★ 4.1k • written 11 weeks ago by • 0
4
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5
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794
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DESeq Input from Salmon + tximport/tximeta
tximportData summarizeToGene tximport DESeq2 salmon
3 months ago LuciaNhu • 0
0
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4
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687
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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 20 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 3.0 years ago by 43k • written 3.1 years ago by • 0
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3
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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 3.6 years ago by 43k • written 3.7 years ago by • 0
0
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1
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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
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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1.9k
views
[DESeq2] Different results from tutorial
deseq2 tximportdata tximport
updated 6.8 years ago by 43k • written 6.8 years ago by • 0
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
views
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
0
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1
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1.9k
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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 ▴ 10
0
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7
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2.0k
views
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
Comment: how many significant figures are there in DESeq2 output by ATpoint ★ 4.7k
If you want consistency then use a fixed software environment like Docker, wirh fixed code and thresholds that make sense. Rounding to near…
Comment: Compare TCGA-PAAD with GTEx gene expression by Jane • 0
why aren't there any answers?
Comment: Too many significant genes when integrating gtex and tcga by Jane • 0
I encountered the same issue: too many DEGs after limma analysis. It is sad that until today we can still see the paper published where GTE…
Comment: how many significant figures are there in DESeq2 output by Matthew McCormack ▴ 180
Thank you for your reply. It is good to know that cutoff of 0.05 means less than 0.05. My concerns are about consistency and reproducibili…
Comment: DiffBind edgeR normalization --- why are the normalization factors all equal to by ATpoint ★ 4.7k
No, normalization factors from edgeR rather than size factors from DESeq2 are not proportional, it's a different concept and implementation…
Votes
A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct
Answer: Group-specific condition effects with individuals nested: matrix is not full ra
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