Showing : txImport • reset
0
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3
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432
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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
2
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5
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336
views
from kallisto to deseq2 analysis
biomaRt DESeq2 tximport
4 months ago Marianna • 0
4
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3
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2.2k
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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
1
vote
4
replies
635
views
tximport from Galaxy output
normalization tximport
updated 6 months ago by • 0 • written 3.0 years 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
0
votes
2
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302
views
tximport ERROR : all(file.exists(files)) is not TRUE
Linux R tximport
4 months ago nakane_clan • 0
1
vote
3
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648
views
tximport error: all(txId == raw[[txIdCol]]) is not TRUE
tximport
8 months ago • updated 7 months ago nicolette.sipperly • 0
2
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4
replies
213
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confused with tximport counts abundance using salmon input
RNASeq tximport
12 weeks ago Al90 • 0
2
votes
3
replies
432
views
importing RSEM isoform to Gene Name with tximport
tximport
updated 12 months ago by 60k • written 12 months ago by ▴ 10
0
votes
2
replies
408
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
0
votes
1
reply
171
views
tximport
salmon tximport
updated 5 months ago by 37k • written 5 months ago by • 0
0
votes
1
reply
478
views
tximport samples with separate tx2gene maps
tximport
updated 7 months ago by 37k • written 8 months ago by • 0
0
votes
1
reply
132
views
Function Request for Rsubread or tximport: parsing command-line featureCounts output
tximport Rsubread
updated 6 weeks ago by ★ 1.3k • written 6 weeks ago by ▴ 10
2
votes
3
replies
203
views
Problem with tximport IDs
tximport tx2gene rnas DESeq2 RNASeqData
8 weeks ago Maka • 0
1
vote
2
replies
326
views
tximeta countsFromAbundance for downstream analysis
tximeta tximport
11 months ago paulimer • 0
0
votes
1
reply
206
views
Ensembl dataset version
tximport rna rnaseqGene biomaRt
updated 5 months ago by ★ 1.3k • written 5 months ago by • 0
2
votes
3
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262
views
Import RSEM output without sample data
DESeq2 tximportData tximport
updated 4 months ago by 37k • written 4 months ago by • 0
1
vote
3
replies
252
views
miRNA differential expression analysis - treat as transcript level?
tximport DESeq2 edgeR swish miRNA
updated 7 days ago by 37k • written 12 days ago by • 0
0
votes
1
reply
118
views
Why TxImport Abundance is slightly different from manually added TPMs?
tximport R
updated 7 weeks ago by 37k • written 8 weeks ago by • 0
0
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4
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532
views
Filtering output from tximport
tximport Salmon
updated 7 months ago by 37k • written 7 months ago by • 0
2
votes
1
reply
302
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
1
vote
7
replies
201
views
RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM tximport scRNAseq DESeq2
updated 2 days ago by 37k • written 9 days ago by • 0
6
votes
2
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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
0
votes
4
replies
73
views
Alternative for wininet method in tximeta
DESeq2 tximport tximportData tximeta
2 days ago uhlkatie • 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 8 months ago by • 0 • written 5.1 years ago by ▴ 40
25 results • Page 1 of 1
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Comment: Error by ATpoint ★ 1.3k
https://github.com/conda-forge/rpy2-feedstock/issues/1
Comment: Error: BiocParallel errors by lxl13260684135 • 0
I came across the same problem, have you solved it?
Answer: How to get DESeq2 results for a list of genes by ATpoint ★ 1.3k
Standard rules apply for filtering in R. If the genes are the rownames of the results object `res` then: res[my_ges,] or if the colu…
Answer: ComplexHeatmap: Change font size of annotation axis values by nalaspina • 0
Someone on the original post was kind enough to provide the answer (in bold below): row_ha = rowAnnotation(foo2 = runif(10), bar2 = anno…
Answer: setting sizeFactors from scran :: caculateSumFactors. by ATpoint ★ 1.3k
You can conveniently convert your SingleCellExperiment to a DESeqDataSet, see https://bioconductor.org/packages/devel/bioc/vignettes/scran/…
Votes
How to get DESeq2 results for a list of genes
Answer: setting sizeFactors from scran :: caculateSumFactors.
Answer: ComplexHeatmap: Change font size of annotation axis values
Comment: package 'BiocInstaller' is not available (for R version 3.4.4)
A: svaseq: how many and which surrogate variables to pick
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