Showing : txImport • reset
0
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1
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586
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discrepancy in IDs from file and tx2gene (IDs don't match)
tximport DESeq2
updated 6 months ago by 68k • written 6 months ago by • 0
0
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1
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769
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Which GTF file to use for creation of tx2gene files?
tximport
updated 7 months ago by 43k • written 7 months ago by • 0
0
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3
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1.1k
views
Many transcripts missing from tx2gene created from Ensembl GTF file
kallisto tximport ensembl
updated 6 months ago by • 0 • written 7 months ago by • 0
0
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1
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505
views
Best tximport quant.genes.sf
tximport tximeta Bioconductor
updated 8 months ago by ★ 5.0k • written 8 months ago by • 0
0
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4
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1.6k
views
Error in H5Dclose(h5dataset) when trying to read in kallisto h5 files
tximport rhdf5
9 months ago Sofia • 0
0
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4
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919
views
Using tximport for kallisto aligned TOIL data
kallisto tximport TOIL
10 months ago Nicholas • 0
0
votes
11
replies
1.6k
views
Problems with oarfish + tximport + swish
fishpond tximport tximeta
updated 12 months ago by • 0 • written 12 months ago by • 0
1
vote
2
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1.3k
views
Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport DESeq2 GSVA
13 months ago georgii.vdovin • 0
4
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5
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1.5k
views
DESeq Input from Salmon + tximport/tximeta
tximportData summarizeToGene tximport DESeq2 salmon
14 months ago LuciaNhu • 0
0
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2
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803
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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 15 months ago by 43k • written 15 months ago by • 0
0
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2
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795
views
tximport data import
tximport
updated 16 months ago by 43k • written 16 months ago by • 0
1
vote
2
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1.4k
views
How to use specific size factors and average transcript lengths from tximport in DESeq2?
DESeq2 tximport
17 months ago grothmn • 0
1
vote
2
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2.9k
views
using tximport with STAR transcript-quantification output
tximport deseq2 STAR
updated 19 months ago by ▴ 40 • written 6.2 years ago by • 0
0
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4
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1.0k
views
Create count matrix from multible quant sf files from different directories
tximportData tximport salmon
19 months ago JG13 • 0
0
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2
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1.0k
views
edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
21 months ago Marianna ▴ 20
0
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2
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1.2k
views
Clarification on Library Size Normalization After Using tximport with countsFromAbundance="lengthScaledTPM"
tximport
updated 22 months ago by 43k • written 22 months ago by • 0
2
votes
1
reply
855
views
Creating data matrix in Deseq2 from tximport data invalid class SummarizedExperiment object
DESeq2 tximport
updated 22 months ago by ★ 5.0k • written 22 months ago by • 0
2
votes
3
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3.9k
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR tximport RNASeq DESeq2
updated 2.1 years ago by ★ 1.4k • written 2.1 years ago by • 0
0
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1
reply
1.2k
views
tximport error with rsem files
rsem tximport
updated 2.1 years ago by ★ 5.0k • written 2.1 years ago by • 0
3
votes
2
replies
1.4k
views
tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
tximport DESeq2
updated 2.1 years ago by 68k • written 2.1 years ago by • 0
0
votes
3
replies
1.3k
views
Tximport Error - transcripts in quant files are not the same as tx2gene
salmon tximport deseq2
updated 2.3 years ago by 43k • written 2.3 years ago by • 0
10
votes
11
replies
3.7k
views
tximport error: vroom
tximport
updated 2.2 years ago by • 0 • written 2.3 years ago by ▴ 40
2
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3
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1.6k
views
Import Salmon data with tximport and pool technical replicates
tximport edgeR
written 2.4 years ago by • 0
5
votes
13
replies
4.8k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport DESeq2
updated 2.3 years ago by 43k • written 2.4 years ago by • 0
2
votes
4
replies
2.1k
views
Handle zero effective gene length when tximport RSEM results
tximport edgeR
updated 2.4 years ago by 43k • written 2.4 years ago by ▴ 10
1
vote
2
replies
2.8k
views
IsoformSwitchAnalyzeR: What are the SV values created in design matrix?
salmon IsoformSwitchAnalyzeR tximport RNASeqData
updated 2.5 years ago by ▴ 120 • written 2.5 years ago by ▴ 10
2
votes
9
replies
2.5k
views
Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport tximportData DESeq2
2.5 years ago Ndimensional ▴ 20
0
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2
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1.3k
views
tximport error in reading salmon output files?
tximport tximportData
updated 23 months ago by • 0 • written 2.6 years ago by • 0
0
votes
1
reply
1.2k
views
Which file in tximport should I use for DESeq2 analysis?
tximport DESeq2
updated 2.7 years ago by 68k • written 2.7 years ago by • 0
2
votes
1
reply
1.5k
views
scaledTPM for DESeq2 using tximport
DESeq2 tximport
updated 2.7 years ago by 43k • written 2.7 years ago by • 0
3
votes
7
replies
2.1k
views
failed to use tximport for creating count matrix from kallisto
tximport kallisto
2.7 years ago Yijing • 0
0
votes
2
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1.7k
views
Error in H5Fopen
rhdf5 Rhdf5lib kallisto tximport
2.7 years ago Yijing • 0
1
vote
3
replies
1.7k
views
tximport error
tximport r
updated 2.7 years ago by 43k • written 2.7 years ago by • 0
0
votes
2
replies
1.8k
views
combining multiple salmon runs after tximport
tximport RNASeq salmon
updated 2.9 years ago by ★ 5.0k • written 2.9 years ago by • 0
1
vote
5
replies
2.1k
views
tximport: kallisto + GENCODE transcript sanitization
tximport
updated 2.9 years ago by 43k • written 2.9 years ago by ▴ 90
6
votes
10
replies
4.4k
views
Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
updated 21 months ago by • 0 • written 2.9 years ago by ▴ 10
0
votes
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 3.0 years ago by ★ 1.6k • written 3.0 years ago by ▴ 10
0
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2
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1.6k
views
how to match salmon output to txname
GenomicFeatures tximport salmon
written 3.0 years ago by • 0
0
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1
reply
1.5k
views
Missing transcript
DESeq2 tximport salmon
updated 3.0 years ago by ★ 5.0k • written 3.0 years ago by • 0
2
votes
5
replies
2.8k
views
Normalizing Salmon output count data matrix using DESeq2
DESeq2 tximport counts Salmon
updated 23 months ago by 43k • written 3.1 years ago by • 0
0
votes
2
replies
1.4k
views
Differentially expression analysis of orthologous genes between two species
DESeq2 tximport
3.1 years ago Konstantinos • 0
2
votes
3
replies
2.3k
views
Error while reading rsem files in tximport
DESeq2 tximport rsem RNASeq tximportData
3.1 years ago mohammedtoufiq91 ▴ 10
4
votes
3
replies
2.0k
views
tx2gene object trouble when working with kallisto and A.thaliana
tx2gene tximport Arabidopsis_thaliana kallisto
updated 3.2 years ago by 68k • written 3.2 years ago by ▴ 10
0
votes
1
reply
1.6k
views
Trouble with importing transcript counts with Salmon
Salmon tximport RNAseq EdgeR
updated 3.2 years ago by ★ 5.0k • written 3.2 years ago by • 0
1
vote
2
replies
1.4k
views
error loading kallisto output in tximport
file.exists false kallisto tximport
3.2 years ago cta • 0
2
votes
3
replies
2.7k
views
How to convert transcript counts to gene counts in R?
DESeq2 tximport
updated 8 months ago by • 0 • written 3.2 years ago by ▴ 50
3
votes
3
replies
1.8k
views
What is the correct way to import transcript abundances from 3' Quantseq results that calculated by kallisto?
tximport tximportData Quantseq kallisto
3.3 years ago • updated 3.2 years ago duhwa.lee • 0
1
vote
2
replies
2.7k
views
transcripts missing from tx2gene
tximport
3.3 years ago Erick • 0
0
votes
1
reply
1.1k
views
tximport: not all(file.exists(files)) are true
tximport
updated 3.3 years ago by 43k • written 3.3 years ago by • 0
3
votes
1
reply
4.3k
views
Understanding tximport working with salmon outputs
Transcriptomics tximport
updated 3.3 years ago by ★ 5.0k • written 3.3 years ago by ▴ 10
297 results • Page 1 of 6
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Comment: DESeq2 - how many surrogate variables from svaseq, use of lfcshrink by ja569116 • 0
Hi @atpoint Thanks for the information. Could you please expand on when to use adjusted p-values vs nominal p-values. My understanding was …
Answer: limpa analysis advice by Gordon Smyth 53k
It is actually very hard to estimate the DPC from observed data, because the curve is function of unobserved intensities rather than a func…
Answer: When to use edgeR or limma by Gordon Smyth 53k
The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
I updated the above answer today.
Answer: When to use edgeR or limma by James W. MacDonald 68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
Votes
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
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