Showing : Tximport • reset
0
votes
1
reply
407
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discrepancy in IDs from file and tx2gene (IDs don't match)
tximport DESeq2
updated 7 weeks ago by 68k • written 7 weeks ago by • 0
0
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1
reply
613
views
Which GTF file to use for creation of tx2gene files?
tximport
updated 10 weeks ago by 43k • written 10 weeks ago by • 0
0
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3
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857
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Many transcripts missing from tx2gene created from Ensembl GTF file
kallisto tximport ensembl
updated 9 weeks ago by • 0 • written 10 weeks ago by • 0
0
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1
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379
views
Best tximport quant.genes.sf
tximport tximeta Bioconductor
updated 3 months ago by ★ 4.9k • written 3 months ago by • 0
0
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4
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1.4k
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Error in H5Dclose(h5dataset) when trying to read in kallisto h5 files
tximport rhdf5
5 months ago Sofia • 0
0
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4
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758
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Using tximport for kallisto aligned TOIL data
kallisto tximport TOIL
5 months ago Nicholas • 0
0
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11
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1.2k
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Problems with oarfish + tximport + swish
fishpond tximport tximeta
updated 7 months ago by • 0 • written 7 months ago by • 0
1
vote
2
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1.0k
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Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport DESeq2 GSVA
8 months ago georgii.vdovin • 0
4
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5
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1.2k
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DESeq Input from Salmon + tximport/tximeta
tximportData summarizeToGene tximport DESeq2 salmon
10 months ago LuciaNhu • 0
0
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2
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636
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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 11 months ago by 43k • written 11 months ago by • 0
0
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2
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618
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tximport data import
tximport
updated 12 months ago by 43k • written 12 months ago by • 0
1
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2
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1.2k
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How to use specific size factors and average transcript lengths from tximport in DESeq2?
DESeq2 tximport
13 months ago grothmn • 0
1
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2
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2.6k
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using tximport with STAR transcript-quantification output
tximport deseq2 STAR
updated 15 months ago by ▴ 40 • written 5.8 years ago by • 0
0
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4
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870
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Create count matrix from multible quant sf files from different directories
tximportData tximport salmon
15 months ago JG13 • 0
0
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2
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843
views
edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
17 months ago Marianna ▴ 20
0
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2
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925
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Clarification on Library Size Normalization After Using tximport with countsFromAbundance="lengthScaledTPM"
tximport
updated 17 months ago by 43k • written 17 months ago by • 0
2
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1
reply
744
views
Creating data matrix in Deseq2 from tximport data invalid class SummarizedExperiment object
DESeq2 tximport
updated 17 months ago by ★ 4.9k • written 17 months ago by • 0
2
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3
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3.4k
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR tximport RNASeq DESeq2
updated 20 months ago by ★ 1.4k • written 21 months ago by • 0
0
votes
1
reply
1.0k
views
tximport error with rsem files
rsem tximport
updated 20 months ago by ★ 4.9k • written 20 months ago by • 0
3
votes
2
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1.2k
views
tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
tximport DESeq2
updated 21 months ago by 68k • written 21 months ago by • 0
0
votes
3
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1.2k
views
Tximport Error - transcripts in quant files are not the same as tx2gene
salmon tximport deseq2
updated 22 months ago by 43k • written 22 months ago by • 0
10
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11
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3.4k
views
tximport error: vroom
tximport
updated 22 months ago by • 0 • written 23 months ago by ▴ 40
2
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3
replies
1.5k
views
Import Salmon data with tximport and pool technical replicates
tximport edgeR
written 2.0 years ago by • 0
5
votes
13
replies
4.0k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport DESeq2
updated 23 months ago by 43k • written 2.0 years ago by • 0
2
votes
4
replies
1.9k
views
Handle zero effective gene length when tximport RSEM results
tximport edgeR
updated 2.0 years ago by 43k • written 2.0 years ago by ▴ 10
1
vote
2
replies
2.6k
views
IsoformSwitchAnalyzeR: What are the SV values created in design matrix?
salmon IsoformSwitchAnalyzeR tximport RNASeqData
updated 2.1 years ago by ▴ 120 • written 2.1 years ago by ▴ 10
2
votes
9
replies
2.2k
views
Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport tximportData DESeq2
2.2 years ago Ndimensional ▴ 20
0
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2
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1.2k
views
tximport error in reading salmon output files?
tximport tximportData
updated 19 months ago by • 0 • written 2.2 years ago by • 0
0
votes
1
reply
1.1k
views
Which file in tximport should I use for DESeq2 analysis?
tximport DESeq2
updated 2.3 years ago by 68k • written 2.3 years ago by • 0
2
votes
1
reply
1.4k
views
scaledTPM for DESeq2 using tximport
DESeq2 tximport
updated 2.3 years ago by 43k • written 2.3 years ago by • 0
3
votes
7
replies
1.9k
views
failed to use tximport for creating count matrix from kallisto
tximport kallisto
2.3 years ago Yijing • 0
0
votes
2
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1.6k
views
Error in H5Fopen
rhdf5 Rhdf5lib kallisto tximport
2.4 years ago • updated 2.3 years ago Yijing • 0
1
vote
3
replies
1.5k
views
tximport error
tximport r
updated 2.4 years ago by 43k • written 2.4 years ago by • 0
0
votes
2
replies
1.6k
views
combining multiple salmon runs after tximport
tximport RNASeq salmon
updated 2.5 years ago by ★ 4.9k • written 2.5 years ago by • 0
1
vote
5
replies
1.9k
views
tximport: kallisto + GENCODE transcript sanitization
tximport
updated 2.5 years ago by 43k • written 2.5 years ago by ▴ 90
6
votes
10
replies
3.9k
views
Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
updated 16 months ago by • 0 • written 2.6 years ago by ▴ 10
0
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1
reply
1.2k
views
Is it possible to convert transcript-level to gene-level dataset to use it in DESeq2 ?
DESeq2 Transcriptomics tximport deseq txi
updated 2.6 years ago by ★ 1.6k • written 2.6 years ago by ▴ 10
0
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2
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1.5k
views
how to match salmon output to txname
GenomicFeatures tximport salmon
written 2.6 years ago by • 0
0
votes
1
reply
1.3k
views
Missing transcript
DESeq2 tximport salmon
updated 2.7 years ago by ★ 4.9k • written 2.7 years ago by • 0
2
votes
5
replies
2.5k
views
Normalizing Salmon output count data matrix using DESeq2
DESeq2 tximport counts Salmon
updated 18 months ago by 43k • written 2.7 years ago by • 0
0
votes
2
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1.3k
views
Differentially expression analysis of orthologous genes between two species
DESeq2 tximport
2.8 years ago Konstantinos • 0
2
votes
3
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2.1k
views
Error while reading rsem files in tximport
DESeq2 tximport rsem RNASeq tximportData
2.8 years ago mohammedtoufiq91 ▴ 10
4
votes
3
replies
1.8k
views
tx2gene object trouble when working with kallisto and A.thaliana
tx2gene tximport Arabidopsis_thaliana kallisto
updated 2.8 years ago by 68k • written 2.8 years ago by ▴ 10
0
votes
1
reply
1.4k
views
Trouble with importing transcript counts with Salmon
Salmon tximport RNAseq EdgeR
updated 2.8 years ago by ★ 4.9k • written 2.8 years ago by • 0
1
vote
2
replies
1.3k
views
error loading kallisto output in tximport
file.exists false kallisto tximport
2.8 years ago cta • 0
2
votes
3
replies
2.5k
views
How to convert transcript counts to gene counts in R?
DESeq2 tximport
updated 4 months ago by • 0 • written 2.9 years ago by ▴ 50
3
votes
3
replies
1.7k
views
What is the correct way to import transcript abundances from 3' Quantseq results that calculated by kallisto?
tximport tximportData Quantseq kallisto
2.9 years ago • updated 2.8 years ago duhwa.lee • 0
1
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2
replies
2.5k
views
transcripts missing from tx2gene
tximport
3.0 years ago • updated 2.9 years ago Erick • 0
0
votes
1
reply
1.1k
views
tximport: not all(file.exists(files)) are true
tximport
updated 3.0 years ago by 43k • written 3.0 years ago by • 0
3
votes
1
reply
3.7k
views
Understanding tximport working with salmon outputs
Transcriptomics tximport
updated 3.0 years ago by ★ 4.9k • written 3.0 years ago by ▴ 10
297 results • Page 1 of 6
Recent ...
Replies
Answer: ROAST compare results with complex design by James W. MacDonald 68k
You are specifying that the last column of your design should be used as the contrast. You should instead use `contrast[,1]`, which will us…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by James W. MacDonald 68k
Yes. You can infer that by figuring out what each coefficient measures. Here is your design matrix: ``` > targets ID Name phase G…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by snijesh ▴ 200
I would like to clarify whether the command `res <- results(dds, name = "phaseLP.conditionTreated")` is the correct approach to generate …
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by James W. MacDonald 68k
Not sure I understand. You ask how to do something and then show how one would do so.
Comment: DiffBind getting Fold values of near 0 by littlefishes20 ▴ 10
Same issues. All peaks return to a fold near 0, although they are significant when visualizing in IGV. Please find the MAplot and volcanoPl…
Votes
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
Can NanoString data be analyzed using DESeq2?
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