Showing : tximport • reset
0
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4
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4.3k
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Importing multiple .h5 files using tximport
Tutorial tximport
updated 5 months ago by 43k • written 7.8 years ago by ▴ 10
0
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1
reply
655
views
discrepancy in IDs from file and tx2gene (IDs don't match)
tximport DESeq2
updated 7 months ago by 68k • written 7 months ago by • 0
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3
replies
1.2k
views
Many transcripts missing from tx2gene created from Ensembl GTF file
kallisto tximport ensembl
updated 8 months ago by • 0 • written 8 months ago by • 0
0
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1
reply
811
views
Which GTF file to use for creation of tx2gene files?
tximport
updated 8 months ago by 43k • written 8 months ago by • 0
5
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5
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4.1k
views
Cannot extract size factor from DESeq2 analysis
deseq2 tximport
updated 9 months ago by 43k • written 5.9 years ago by • 0
0
votes
1
reply
684
views
Best tximport quant.genes.sf
tximport tximeta Bioconductor
updated 9 months ago by ★ 5.0k • written 9 months ago by • 0
2
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3
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2.8k
views
How to convert transcript counts to gene counts in R?
DESeq2 tximport
updated 10 months ago by • 0 • written 3.4 years ago by ▴ 50
0
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4
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1.6k
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Error in H5Dclose(h5dataset) when trying to read in kallisto h5 files
tximport rhdf5
11 months ago Sofia • 0
0
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4
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1.0k
views
Using tximport for kallisto aligned TOIL data
kallisto tximport TOIL
12 months ago • updated 11 months ago Nicholas • 0
0
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11
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1.7k
views
Problems with oarfish + tximport + swish
fishpond tximport tximeta
updated 13 months ago by • 0 • written 13 months ago by • 0
6
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7
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4.2k
views
edgeR + tximport: calcNormFactors and the usage of offsets
edgeR tximport differential expression
updated 14 months ago by 53k • written 5.8 years ago by ▴ 20
1
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2
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1.4k
views
Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport DESeq2 GSVA
14 months ago georgii.vdovin • 0
4
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5
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1.7k
views
DESeq Input from Salmon + tximport/tximeta
tximportData summarizeToGene tximport DESeq2 salmon
16 months ago LuciaNhu • 0
0
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2
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849
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How can I obtain DEGs that are resulted from using salmon in alignment-based mode or mapping-based mode?
tximport DESeq2
updated 17 months ago by 43k • written 17 months ago by • 0
0
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2
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851
views
tximport data import
tximport
updated 18 months ago by 43k • written 18 months ago by • 0
1
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2
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1.5k
views
How to use specific size factors and average transcript lengths from tximport in DESeq2?
DESeq2 tximport
19 months ago grothmn • 0
1
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2
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3.1k
views
using tximport with STAR transcript-quantification output
tximport deseq2 STAR
updated 21 months ago by ▴ 40 • written 6.4 years ago by • 0
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4
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1.1k
views
Create count matrix from multible quant sf files from different directories
tximportData tximport salmon
21 months ago JG13 • 0
6
votes
10
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4.9k
views
Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
updated 22 months ago by • 0 • written 3.1 years ago by ▴ 10
0
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2
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1.1k
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edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
23 months ago Marianna ▴ 20
0
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2
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1.3k
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Clarification on Library Size Normalization After Using tximport with countsFromAbundance="lengthScaledTPM"
tximport
updated 23 months ago by 43k • written 23 months ago by • 0
0
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5
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11k
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tximport all(file.exists(files)) is not TRUE
bioconductor tximport rnaseq R
updated 23 months ago by • 0 • written 9.4 years ago by • 0
2
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1
reply
887
views
Creating data matrix in Deseq2 from tximport data invalid class SummarizedExperiment object
DESeq2 tximport
updated 24 months ago by ★ 5.0k • written 24 months ago by • 0
2
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5
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3.0k
views
Normalizing Salmon output count data matrix using DESeq2
DESeq2 tximport counts Salmon
updated 2.0 years ago by 43k • written 3.2 years ago by • 0
0
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2
replies
1.3k
views
tximport error in reading salmon output files?
tximport tximportData
updated 2.1 years ago by • 0 • written 2.7 years ago by • 0
2
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3
replies
4.3k
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR tximport RNASeq DESeq2
updated 2.2 years ago by ★ 1.4k • written 2.2 years ago by • 0
0
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1
reply
1.3k
views
tximport error with rsem files
rsem tximport
updated 2.2 years ago by ★ 5.0k • written 2.2 years ago by • 0
3
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2
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1.4k
views
tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
tximport DESeq2
updated 2.3 years ago by 68k • written 2.3 years ago by • 0
10
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11
replies
3.9k
views
tximport error: vroom
tximport
updated 2.4 years ago by • 0 • written 2.4 years ago by ▴ 40
0
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3
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1.4k
views
Tximport Error - transcripts in quant files are not the same as tx2gene
salmon tximport deseq2
updated 2.4 years ago by 43k • written 2.4 years ago by • 0
5
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13
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5.4k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport DESeq2
updated 2.4 years ago by 43k • written 2.5 years ago by • 0
2
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3
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1.7k
views
Import Salmon data with tximport and pool technical replicates
tximport edgeR
written 2.6 years ago by • 0
2
votes
4
replies
2.2k
views
Handle zero effective gene length when tximport RSEM results
tximport edgeR
updated 2.5 years ago by 43k • written 2.5 years ago by ▴ 10
1
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2
replies
2.9k
views
IsoformSwitchAnalyzeR: What are the SV values created in design matrix?
salmon IsoformSwitchAnalyzeR tximport RNASeqData
updated 2.6 years ago by ▴ 120 • written 2.6 years ago by ▴ 10
16
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25
replies
4.8k
views
dtuScaledTPM vs lengthScaledTPM in DTU analysis
tximport dtu salmon TPM rnaseqDTU
written 6.9 years ago by ▴ 60
1
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5
replies
4.1k
views
tximport error: all(txId == raw[[txIdCol]]) is not TRUE
tximport
updated 2.6 years ago by 43k • written 4.3 years ago by • 0
2
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9
replies
2.6k
views
Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport tximportData DESeq2
2.7 years ago Ndimensional ▴ 20
4
votes
9
replies
5.7k
views
How to get DESeq2 sizefactors from data imported using tximport
deseq2 sailfish tximport
updated 2.8 years ago by • 0 • written 8.7 years ago by • 0
0
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4
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2.0k
views
tximport importer isoform abundance
tximport
updated 2.8 years ago by ▴ 200 • written 5.7 years ago by ▴ 620
0
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1
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1.3k
views
Which file in tximport should I use for DESeq2 analysis?
tximport DESeq2
updated 2.8 years ago by 68k • written 2.8 years ago by • 0
2
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1
reply
1.6k
views
scaledTPM for DESeq2 using tximport
DESeq2 tximport
updated 2.8 years ago by 43k • written 2.8 years ago by • 0
3
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7
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2.2k
views
failed to use tximport for creating count matrix from kallisto
tximport kallisto
2.8 years ago Yijing • 0
0
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2
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1.8k
views
Error in H5Fopen
rhdf5 Rhdf5lib kallisto tximport
2.9 years ago • updated 2.8 years ago Yijing • 0
1
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3
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1.8k
views
tximport error
tximport r
updated 2.9 years ago by 43k • written 2.9 years ago by • 0
0
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2
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1.9k
views
combining multiple salmon runs after tximport
tximport RNASeq salmon
updated 3.0 years ago by ★ 5.0k • written 3.0 years ago by • 0
1
vote
5
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2.3k
views
tximport: kallisto + GENCODE transcript sanitization
tximport
updated 3.1 years ago by 43k • written 3.1 years ago by ▴ 90
0
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1
reply
1.3k
views
Is it possible to convert transcript-level to gene-level dataset to use it in DESeq2 ?
DESeq2 Transcriptomics tximport deseq txi
updated 3.1 years ago by ★ 1.6k • written 3.1 years ago by ▴ 10
0
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2
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1.7k
views
how to match salmon output to txname
GenomicFeatures tximport salmon
written 3.2 years ago by • 0
0
votes
1
reply
1.5k
views
Missing transcript
DESeq2 tximport salmon
updated 3.2 years ago by ★ 5.0k • written 3.2 years ago by • 0
0
votes
2
replies
1.5k
views
Differentially expression analysis of orthologous genes between two species
DESeq2 tximport
3.3 years ago Konstantinos • 0
297 results • Page 1 of 6
Recent ...
Replies
Comment: GSEA error by Adithi • 0
Thank you so much. That makes perfect sense to me. I will work on this.
Comment: tximeta cannot open annotation gtf? by Michael Love 43k
Yes, so this is the same type of error you would get if you tried to assemble a *SummarizedExperiment* manually with tximport + GTF process…
Answer: tximeta cannot open annotation gtf? by ATpoint ★ 5.0k
> Timeout of 60 seconds was reached You have to increase the default timeout limits for downloads, `options(timeout=3600)`. GENCODE serve…
Answer: GSEA error by James W. MacDonald 68k
At a very high level, the way non-model organisms are annotated is by using blast to find orthologs in other species that are well annotate…
Comment: Unable to find ENTREZ IDs by Adithi • 0
Hi James, Thank you so much for your reply. My main goal is to find ortholog genes from chinese hamster gene symbols to mouse gene symbols…
Votes
Answer: GSEA error
Answer: OrgDb for maize
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
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