Showing : tximport • reset
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Best tximport quant.genes.sf
tximport tximeta Bioconductor
updated 7 days ago by ★ 4.8k • written 8 days ago by • 0
0
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4
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1.2k
views
Error in H5Dclose(h5dataset) when trying to read in kallisto h5 files
tximport rhdf5
7 weeks ago • updated 6 weeks ago Sofia • 0
0
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4
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610
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Using tximport for kallisto aligned TOIL data
kallisto tximport TOIL
10 weeks ago • updated 9 weeks ago Nicholas • 0
0
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11
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961
views
Problems with oarfish + tximport + swish
fishpond tximport tximeta
updated 3 months ago by • 0 • written 4 months ago by • 0
1
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2
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866
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Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport DESeq2 GSVA
5 months ago georgii.vdovin • 0
4
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5
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1.0k
views
DESeq Input from Salmon + tximport/tximeta
tximportData summarizeToGene tximport DESeq2 salmon
6 months ago LuciaNhu • 0
0
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2
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555
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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 7 months ago by 43k • written 7 months ago by • 0
0
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2
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537
views
tximport data import
tximport
updated 8 months ago by 43k • written 8 months ago by • 0
1
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2
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1.1k
views
How to use specific size factors and average transcript lengths from tximport in DESeq2?
DESeq2 tximport
9 months ago grothmn • 0
1
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2
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2.5k
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using tximport with STAR transcript-quantification output
tximport deseq2 STAR
updated 11 months ago by ▴ 40 • written 5.6 years ago by • 0
0
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4
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765
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Create count matrix from multible quant sf files from different directories
tximportData tximport salmon
11 months ago JG13 • 0
0
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2
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727
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edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
13 months ago Marianna ▴ 20
0
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2
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809
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Clarification on Library Size Normalization After Using tximport with countsFromAbundance="lengthScaledTPM"
tximport
updated 13 months ago by 43k • written 13 months ago by • 0
2
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1
reply
665
views
Creating data matrix in Deseq2 from tximport data invalid class SummarizedExperiment object
DESeq2 tximport
updated 14 months ago by ★ 4.8k • written 14 months ago by • 0
2
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3
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3.2k
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR tximport RNASeq DESeq2
updated 17 months ago by ★ 1.4k • written 17 months ago by • 0
0
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1
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887
views
tximport error with rsem files
rsem tximport
updated 17 months ago by ★ 4.8k • written 17 months ago by • 0
3
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2
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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
0
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3
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1.0k
views
Tximport Error - transcripts in quant files are not the same as tx2gene
salmon tximport deseq2
updated 19 months ago by 43k • written 19 months ago by • 0
10
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11
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3.2k
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tximport error: vroom
tximport
updated 19 months ago by • 0 • written 19 months ago by ▴ 40
2
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3
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1.4k
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Import Salmon data with tximport and pool technical replicates
tximport edgeR
written 21 months ago by • 0
5
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13
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3.7k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport DESeq2
updated 20 months ago by 43k • written 20 months ago by • 0
2
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4
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1.8k
views
Handle zero effective gene length when tximport RSEM results
tximport edgeR
updated 20 months ago by 43k • written 21 months ago by ▴ 10
1
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2
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2.5k
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IsoformSwitchAnalyzeR: What are the SV values created in design matrix?
salmon IsoformSwitchAnalyzeR tximport RNASeqData
updated 21 months ago by ▴ 120 • written 22 months ago by ▴ 10
2
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9
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2.0k
views
Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport tximportData DESeq2
22 months ago Ndimensional ▴ 20
0
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2
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1.1k
views
tximport error in reading salmon output files?
tximport tximportData
updated 15 months ago by • 0 • written 23 months ago by • 0
0
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1
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1.0k
views
Which file in tximport should I use for DESeq2 analysis?
tximport DESeq2
updated 2.0 years ago by 68k • written 2.0 years ago by • 0
2
votes
1
reply
1.2k
views
scaledTPM for DESeq2 using tximport
DESeq2 tximport
updated 2.0 years ago by 43k • written 2.0 years ago by • 0
3
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7
replies
1.7k
views
failed to use tximport for creating count matrix from kallisto
tximport kallisto
2.0 years ago Yijing • 0
0
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2
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1.4k
views
Error in H5Fopen
rhdf5 Rhdf5lib kallisto tximport
2.1 years ago • updated 2.0 years ago Yijing • 0
1
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3
replies
1.5k
views
tximport error
tximport r
updated 2.1 years ago by 43k • written 2.1 years ago by • 0
0
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2
replies
1.6k
views
combining multiple salmon runs after tximport
tximport RNASeq salmon
updated 2.2 years ago by ★ 4.8k • written 2.3 years ago by • 0
1
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5
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1.8k
views
tximport: kallisto + GENCODE transcript sanitization
tximport
updated 2.3 years ago by 43k • written 2.3 years ago by ▴ 90
6
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10
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3.6k
views
Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
updated 13 months ago by • 0 • written 2.3 years ago by ▴ 10
0
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1
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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
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2
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1.4k
views
how to match salmon output to txname
GenomicFeatures tximport salmon
written 2.4 years ago by • 0
0
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1
reply
1.2k
views
Missing transcript
DESeq2 tximport salmon
updated 2.4 years ago by ★ 4.8k • written 2.4 years ago by • 0
2
votes
5
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2.4k
views
Normalizing Salmon output count data matrix using DESeq2
DESeq2 tximport counts Salmon
updated 15 months ago by 43k • written 2.4 years ago by • 0
0
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2
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1.2k
views
Differentially expression analysis of orthologous genes between two species
DESeq2 tximport
2.5 years ago Konstantinos • 0
2
votes
3
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1.9k
views
Error while reading rsem files in tximport
DESeq2 tximport rsem RNASeq tximportData
2.5 years ago mohammedtoufiq91 ▴ 10
4
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3
replies
1.7k
views
tx2gene object trouble when working with kallisto and A.thaliana
tx2gene tximport Arabidopsis_thaliana kallisto
updated 2.5 years ago by 68k • written 2.5 years ago by ▴ 10
0
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1
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1.3k
views
Trouble with importing transcript counts with Salmon
Salmon tximport RNAseq EdgeR
updated 2.5 years ago by ★ 4.8k • written 2.5 years ago by • 0
1
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2
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1.2k
views
error loading kallisto output in tximport
file.exists false kallisto tximport
2.5 years ago cta • 0
2
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3
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2.3k
views
How to convert transcript counts to gene counts in R?
DESeq2 tximport
updated 26 days ago by • 0 • written 2.6 years ago by ▴ 50
3
votes
3
replies
1.6k
views
What is the correct way to import transcript abundances from 3' Quantseq results that calculated by kallisto?
tximport tximportData Quantseq kallisto
2.6 years ago • updated 2.5 years ago duhwa.lee • 0
1
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2
replies
2.4k
views
transcripts missing from tx2gene
tximport
2.7 years ago Erick • 0
0
votes
1
reply
997
views
tximport: not all(file.exists(files)) are true
tximport
updated 2.7 years ago by 43k • written 2.7 years ago by • 0
3
votes
1
reply
3.5k
views
Understanding tximport working with salmon outputs
Transcriptomics tximport
updated 2.7 years ago by ★ 4.8k • written 2.7 years ago by ▴ 10
3
votes
4
replies
2.2k
views
difference between txi$counts and txi$abundance when countsFromAbundance is true
RNAseq tximport
updated 2.7 years ago by ★ 4.8k • written 2.7 years ago by • 0
0
votes
3
replies
1.4k
views
tximport error
error tximport
updated 2.7 years ago by 43k • written 2.7 years ago by • 0
5
votes
6
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2.3k
views
Selecting individual samples from tximport and DGE matrix design with missing biological replicate
DESeq2 limma tximport
updated 2.7 years ago by 52k • written 2.7 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: Limma suqeezeVar by Gordon Smyth 52k
I am not quite clear why you're not using the limma package directly, because it will compute all the variances and the df automatically fo…
Comment: Discrepancies in normalised count data vs unnormalised by swbarnes2 ★ 1.4k
Well, that's going to make each sample normalize quite differently. So you should expect large difference between normalized and unnormali…
Comment: Can't install BioC packages (and manager) behind firewall by Marcel Ramos 700
Hi Delphine, Please make sure that your SSL certificates are up to date. Check with your system's administrator. Your browser may be usin…
Comment: Limma trend with limpa by Alejandro • 0
Dear Gordon, Thank you very much!
Answer: DESeq2 from phyloseq error by asafpr • 0
Apparently, I left this line: ```r setClassUnion("ExpData", c("matrix", "SummarizedExperiment")) ``` to patch the ExpData issue which was …
Votes
Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
Comment: Check removeBatchEffect effectiveness
Answer: Check removeBatchEffect effectiveness
A: what should I do with many zero counts from Salmon quantification
Comment: parameters of filterByExpr
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