Showing : Tximport • reset
0
votes
2
replies
172
views
edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
4 weeks ago Marianna ▴ 20
0
votes
2
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209
views
Clarification on Library Size Normalization After Using tximport with countsFromAbundance="lengthScaledTPM"
tximport
updated 5 weeks ago by 41k • written 5 weeks ago by • 0
2
votes
1
reply
249
views
Creating data matrix in Deseq2 from tximport data invalid class SummarizedExperiment object
DESeq2 tximport
updated 7 weeks ago by ★ 4.1k • written 7 weeks ago by • 0
2
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3
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1.2k
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR tximport RNASeq DESeq2
updated 4 months ago by ★ 1.3k • written 4 months ago by • 0
0
votes
1
reply
354
views
tximport error with rsem files
rsem tximport
updated 4 months ago by ★ 4.1k • written 4 months ago by • 0
3
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2
replies
564
views
tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
tximport DESeq2
updated 5 months ago by 65k • written 5 months ago by • 0
0
votes
3
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431
views
Tximport Error - transcripts in quant files are not the same as tx2gene
salmon tximport deseq2
updated 6 months ago by 41k • written 6 months ago by • 0
10
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11
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1.9k
views
tximport error: vroom
tximport
updated 6 months ago by • 0 • written 7 months ago by ▴ 40
2
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3
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821
views
Import Salmon data with tximport and pool technical replicates
tximport edgeR
written 8 months ago by • 0
4
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13
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1.4k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport DESeq2
updated 7 months ago by 41k • written 8 months ago by • 0
0
votes
4
replies
888
views
Handle zero effective gene length when tximport RSEM results
tximport edgeR
updated 8 months ago by 41k • written 8 months ago by • 0
1
vote
2
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1.5k
views
IsoformSwitchAnalyzeR: What are the SV values created in design matrix?
salmon IsoformSwitchAnalyzeR tximport RNASeqData
updated 9 months ago by ▴ 120 • written 9 months ago by ▴ 10
2
votes
9
replies
1.2k
views
Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport tximportData DESeq2
10 months ago Ndimensional ▴ 20
0
votes
2
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669
views
tximport error in reading salmon output files?
tximport tximportData
updated 3 months ago by • 0 • written 10 months ago by • 0
0
votes
1
reply
616
views
Which file in tximport should I use for DESeq2 analysis?
tximport DESeq2
updated 11 months ago by 65k • written 11 months ago by • 0
2
votes
1
reply
658
views
scaledTPM for DESeq2 using tximport
DESeq2 tximport
updated 12 months ago by 41k • written 12 months ago by • 0
3
votes
7
replies
1.1k
views
failed to use tximport for creating count matrix from kallisto
tximport kallisto
12 months ago Yijing • 0
6
votes
10
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1.6k
views
Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
updated 17 days ago by • 0 • written 15 months ago by ▴ 10
2
votes
5
replies
1.4k
views
Normalizing Salmon output count data matrix using DESeq2
DESeq2 tximport counts Salmon
updated 10 weeks ago by 41k • written 16 months ago by • 0
1
vote
5
replies
2.8k
views
tximport error: all(txId == raw[[txIdCol]]) is not TRUE
tximport
updated 9 months ago by 41k • written 2.5 years ago by • 0
0
votes
4
replies
1.2k
views
tximport importer isoform abundance
tximport
updated 11 months ago by ▴ 190 • written 3.9 years ago by ▴ 620
16
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25
replies
3.0k
views
dtuScaledTPM vs lengthScaledTPM in DTU analysis
tximport dtu salmon TPM rnaseqDTU
written 5.1 years ago by ▴ 60
4
votes
9
replies
4.4k
views
How to get DESeq2 sizefactors from data imported using tximport
deseq2 sailfish tximport
updated 11 months ago by • 0 • written 6.9 years ago by • 0
0
votes
5
replies
9.3k
views
tximport all(file.exists(files)) is not TRUE
bioconductor tximport rnaseq R
updated 6 weeks ago by • 0 • written 7.6 years ago by • 0
24 results • Page 1 of 1
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Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by Hervé Pagès 16k
Indeed. Calculations involving floating point arithmetic are architecture-dependent, and testing the results should be done with `all.equal…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
I will follow what you suggested. I didn't use max gap anywhere. I was following statistic I and regarding the size of features, my small…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 41k
Oh I see, for the second question, I don't have a great answer. I typically think of one set as the anchor, whose ascertainment is driving …
Comment: Help with running egsea() by James W. MacDonald 65k
Oh, right. Ideally you would use NCBI (aka Entrez gene) IDs because they are way more likely to be unique. Gene symbols are broken down int…
Comment: Help with running egsea() by Chris • 0
Thanks James! I update the question. The last question mean when we use `buildIdx()`, could we use gene symbol instead of entrezID. However…
Votes
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Help with running egsea()
Answer: Trim/Filter out-of-bounds GRanges
Comment: Help with running egsea()
Answer: How to save the DEXSeq results
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