Showing : tximport • reset
2
votes
3
replies
2.3k
views
How to convert transcript counts to gene counts in R?
DESeq2 tximport
updated 5 days ago by • 0 • written 2.5 years ago by ▴ 50
0
votes
4
replies
1.2k
views
Error in H5Dclose(h5dataset) when trying to read in kallisto h5 files
tximport rhdf5
4 weeks ago • updated 27 days ago Sofia • 0
0
votes
4
replies
564
views
Using tximport for kallisto aligned TOIL data
kallisto tximport TOIL
7 weeks ago • updated 5 weeks ago Nicholas • 0
0
votes
11
replies
923
views
Problems with oarfish + tximport + swish
fishpond tximport tximeta
updated 3 months ago by • 0 • written 3 months ago by • 0
6
votes
7
replies
3.5k
views
edgeR + tximport: calcNormFactors and the usage of offsets
edgeR tximport differential expression
updated 3 months ago by 52k • written 5.0 years ago by ▴ 20
1
vote
2
replies
788
views
Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport DESeq2 GSVA
4 months ago georgii.vdovin • 0
4
votes
5
replies
981
views
DESeq Input from Salmon + tximport/tximeta
tximportData summarizeToGene tximport DESeq2 salmon
5 months ago LuciaNhu • 0
0
votes
2
replies
531
views
How can I obtain DEGs that are resulted from using salmon in alignment-based mode or mapping-based mode?
tximport DESeq2
updated 6 months ago by 43k • written 6 months ago by • 0
0
votes
2
replies
523
views
tximport data import
tximport
updated 7 months ago by 43k • written 7 months ago by • 0
1
vote
2
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1.0k
views
How to use specific size factors and average transcript lengths from tximport in DESeq2?
DESeq2 tximport
8 months ago grothmn • 0
1
vote
2
replies
2.5k
views
using tximport with STAR transcript-quantification output
tximport deseq2 STAR
updated 10 months ago by ▴ 40 • written 5.5 years ago by • 0
0
votes
4
replies
744
views
Create count matrix from multible quant sf files from different directories
tximportData tximport salmon
10 months ago JG13 • 0
6
votes
10
replies
3.4k
views
Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
updated 12 months ago by • 0 • written 2.2 years ago by ▴ 10
0
votes
2
replies
711
views
edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
13 months ago • updated 12 months ago Marianna ▴ 20
0
votes
2
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769
views
Clarification on Library Size Normalization After Using tximport with countsFromAbundance="lengthScaledTPM"
tximport
updated 13 months ago by 43k • written 13 months ago by • 0
0
votes
5
replies
11k
views
tximport all(file.exists(files)) is not TRUE
bioconductor tximport rnaseq R
updated 13 months ago by • 0 • written 8.6 years ago by • 0
2
votes
1
reply
644
views
Creating data matrix in Deseq2 from tximport data invalid class SummarizedExperiment object
DESeq2 tximport
updated 13 months ago by ★ 4.8k • written 13 months ago by • 0
2
votes
5
replies
2.3k
views
Normalizing Salmon output count data matrix using DESeq2
DESeq2 tximport counts Salmon
updated 14 months ago by 43k • written 2.3 years ago by • 0
0
votes
2
replies
1.1k
views
tximport error in reading salmon output files?
tximport tximportData
updated 15 months ago by • 0 • written 22 months ago by • 0
2
votes
3
replies
3.1k
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR tximport RNASeq DESeq2
updated 16 months ago by ★ 1.4k • written 16 months ago by • 0
0
votes
1
reply
875
views
tximport error with rsem files
rsem tximport
updated 16 months ago by ★ 4.8k • written 16 months ago by • 0
3
votes
2
replies
1.1k
views
tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
tximport DESeq2
updated 17 months ago by 68k • written 17 months ago by • 0
10
votes
11
replies
3.1k
views
tximport error: vroom
tximport
updated 18 months ago by • 0 • written 19 months ago by ▴ 40
0
votes
3
replies
1.0k
views
Tximport Error - transcripts in quant files are not the same as tx2gene
salmon tximport deseq2
updated 18 months ago by 43k • written 18 months ago by • 0
5
votes
13
replies
3.5k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport DESeq2
updated 19 months ago by 43k • written 20 months ago by • 0
2
votes
3
replies
1.4k
views
Import Salmon data with tximport and pool technical replicates
tximport edgeR
written 20 months ago by • 0
2
votes
4
replies
1.8k
views
Handle zero effective gene length when tximport RSEM results
tximport edgeR
updated 20 months ago by 43k • written 20 months ago by ▴ 10
1
vote
2
replies
2.5k
views
IsoformSwitchAnalyzeR: What are the SV values created in design matrix?
salmon IsoformSwitchAnalyzeR tximport RNASeqData
updated 21 months ago by ▴ 120 • written 21 months ago by ▴ 10
16
votes
25
replies
4.1k
views
dtuScaledTPM vs lengthScaledTPM in DTU analysis
tximport dtu salmon TPM rnaseqDTU
written 6.1 years ago by ▴ 60
1
vote
5
replies
3.7k
views
tximport error: all(txId == raw[[txIdCol]]) is not TRUE
tximport
updated 21 months ago by 43k • written 3.5 years ago by • 0
2
votes
9
replies
2.0k
views
Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport tximportData DESeq2
22 months ago • updated 21 months ago Ndimensional ▴ 20
4
votes
9
replies
5.2k
views
How to get DESeq2 sizefactors from data imported using tximport
deseq2 sailfish tximport
updated 23 months ago by • 0 • written 7.8 years ago by • 0
0
votes
4
replies
1.7k
views
tximport importer isoform abundance
tximport
updated 23 months ago by ▴ 200 • written 4.8 years ago by ▴ 620
0
votes
1
reply
1.0k
views
Which file in tximport should I use for DESeq2 analysis?
tximport DESeq2
updated 23 months ago by 68k • written 23 months ago by • 0
2
votes
1
reply
1.2k
views
scaledTPM for DESeq2 using tximport
DESeq2 tximport
updated 23 months ago by 43k • written 23 months ago by • 0
3
votes
7
replies
1.7k
views
failed to use tximport for creating count matrix from kallisto
tximport kallisto
24 months ago Yijing • 0
0
votes
2
replies
1.4k
views
Error in H5Fopen
rhdf5 Rhdf5lib kallisto tximport
2.0 years ago • updated 24 months ago Yijing • 0
1
vote
3
replies
1.4k
views
tximport error
tximport r
updated 2.0 years ago by 43k • written 2.0 years ago by • 0
0
votes
2
replies
1.5k
views
combining multiple salmon runs after tximport
tximport RNASeq salmon
updated 2.2 years ago by ★ 4.8k • written 2.2 years ago by • 0
1
vote
5
replies
1.8k
views
tximport: kallisto + GENCODE transcript sanitization
tximport
updated 2.2 years ago by 43k • written 2.2 years ago by ▴ 90
0
votes
1
reply
1.1k
views
Is it possible to convert transcript-level to gene-level dataset to use it in DESeq2 ?
DESeq2 Transcriptomics tximport deseq txi
updated 2.3 years ago by ★ 1.6k • written 2.3 years ago by ▴ 10
0
votes
2
replies
1.4k
views
how to match salmon output to txname
GenomicFeatures tximport salmon
written 2.3 years ago by • 0
0
votes
1
reply
1.2k
views
Missing transcript
DESeq2 tximport salmon
updated 2.3 years ago by ★ 4.8k • written 2.3 years ago by • 0
0
votes
2
replies
1.2k
views
Differentially expression analysis of orthologous genes between two species
DESeq2 tximport
2.4 years ago Konstantinos • 0
2
votes
3
replies
1.9k
views
Error while reading rsem files in tximport
DESeq2 tximport rsem RNASeq tximportData
2.4 years ago mohammedtoufiq91 ▴ 10
4
votes
3
replies
1.6k
views
tx2gene object trouble when working with kallisto and A.thaliana
tx2gene tximport Arabidopsis_thaliana kallisto
updated 2.4 years ago by 68k • written 2.4 years ago by ▴ 10
0
votes
4
replies
2.6k
views
Tximport error message - colnames
tximport
written 3.9 years ago by • 0
0
votes
1
reply
1.3k
views
Trouble with importing transcript counts with Salmon
Salmon tximport RNAseq EdgeR
updated 2.4 years ago by ★ 4.8k • written 2.4 years ago by • 0
1
vote
2
replies
1.2k
views
error loading kallisto output in tximport
file.exists false kallisto tximport
2.5 years ago cta • 0
3
votes
3
replies
1.5k
views
What is the correct way to import transcript abundances from 3' Quantseq results that calculated by kallisto?
tximport tximportData Quantseq kallisto
2.5 years ago duhwa.lee • 0
50 results • Page 1 of 1
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Replies
Comment: Bioconductor 3.20 Release Schedule by randyprice13102000 • 0
This offers much info https://bioconductor.org/checkResults/release/bioc-LATEST/
Comment: Filtering after DESeq by ATpoint ★ 4.8k
The problem is that your prefilter is not group-aware so the behaviour of seeing these sorts of outliers is expected. This is why I always …
Comment: GSEA preranked analysis downstream of DEseq2 by ATpoint ★ 4.8k
All due respect, this is what people do since pvalues exist, so this paper is not a reference, not is this a special score that merits a na…
Comment: Check removeBatchEffect effectiveness by ATpoint ★ 4.8k
> insert size, mean GC, etc... This is not a classical "batch" in the common sense, at least I've never seen this to be corrected for expl…
Answer: Check removeBatchEffect effectiveness by Gordon Smyth 52k
Your call to removeBatchEffect() is not correct because that function does not have an argument called `batch3`, meaning that the batch fac…
Votes
Answer: DiffBind; Error: No sites have activity greater than filter value
DiffBind; Error: No sites have activity greater than filter value
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
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