Showing : tximport • reset
6
votes
10
replies
1.8k
views
Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
updated 5 weeks ago by • 0 • written 15 months ago by ▴ 10
0
votes
2
replies
203
views
edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
7 weeks ago Marianna ▴ 20
0
votes
2
replies
225
views
Clarification on Library Size Normalization After Using tximport with countsFromAbundance="lengthScaledTPM"
tximport
updated 8 weeks ago by 42k • written 8 weeks ago by • 0
0
votes
5
replies
9.3k
views
tximport all(file.exists(files)) is not TRUE
bioconductor tximport rnaseq R
updated 9 weeks ago by • 0 • written 7.7 years ago by • 0
2
votes
1
reply
276
views
Creating data matrix in Deseq2 from tximport data invalid class SummarizedExperiment object
DESeq2 tximport
updated 10 weeks ago by ★ 4.2k • written 10 weeks ago by • 0
2
votes
5
replies
1.4k
views
Normalizing Salmon output count data matrix using DESeq2
DESeq2 tximport counts Salmon
updated 3 months ago by 42k • written 17 months ago by • 0
0
votes
2
replies
695
views
tximport error in reading salmon output files?
tximport tximportData
updated 3 months ago by • 0 • written 11 months ago by • 0
2
votes
3
replies
1.3k
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR tximport RNASeq DESeq2
updated 5 months ago by ★ 1.4k • written 5 months ago by • 0
0
votes
1
reply
377
views
tximport error with rsem files
rsem tximport
updated 5 months ago by ★ 4.2k • written 5 months ago by • 0
3
votes
2
replies
597
views
tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
tximport DESeq2
updated 5 months ago by 66k • written 5 months ago by • 0
10
votes
11
replies
2.0k
views
tximport error: vroom
tximport
updated 7 months ago by • 0 • written 7 months ago by ▴ 40
0
votes
3
replies
459
views
Tximport Error - transcripts in quant files are not the same as tx2gene
salmon tximport deseq2
updated 7 months ago by 42k • written 7 months ago by • 0
4
votes
13
replies
1.5k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport DESeq2
updated 8 months ago by 42k • written 9 months ago by • 0
2
votes
3
replies
848
views
Import Salmon data with tximport and pool technical replicates
tximport edgeR
written 9 months ago by • 0
0
votes
4
replies
944
views
Handle zero effective gene length when tximport RSEM results
tximport edgeR
updated 9 months ago by 42k • written 9 months ago by • 0
1
vote
2
replies
1.6k
views
IsoformSwitchAnalyzeR: What are the SV values created in design matrix?
salmon IsoformSwitchAnalyzeR tximport RNASeqData
updated 10 months ago by ▴ 120 • written 10 months ago by ▴ 10
16
votes
25
replies
3.1k
views
dtuScaledTPM vs lengthScaledTPM in DTU analysis
tximport dtu salmon TPM rnaseqDTU
written 5.1 years ago by ▴ 60
1
vote
5
replies
2.9k
views
tximport error: all(txId == raw[[txIdCol]]) is not TRUE
tximport
updated 10 months ago by 42k • written 2.6 years ago by • 0
2
votes
9
replies
1.2k
views
Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport tximportData DESeq2
10 months ago Ndimensional ▴ 20
4
votes
9
replies
4.4k
views
How to get DESeq2 sizefactors from data imported using tximport
deseq2 sailfish tximport
updated 12 months ago by • 0 • written 6.9 years ago by • 0
0
votes
4
replies
1.3k
views
tximport importer isoform abundance
tximport
updated 12 months ago by ▴ 190 • written 3.9 years ago by ▴ 620
0
votes
1
reply
655
views
Which file in tximport should I use for DESeq2 analysis?
tximport DESeq2
updated 12 months ago by 66k • written 12 months ago by • 0
2
votes
1
reply
685
views
scaledTPM for DESeq2 using tximport
DESeq2 tximport
updated 12 months ago by 42k • written 12 months ago by • 0
3
votes
7
replies
1.2k
views
failed to use tximport for creating count matrix from kallisto
tximport kallisto
12 months ago Yijing • 0
0
votes
2
replies
868
views
Error in H5Fopen
rhdf5 Rhdf5lib kallisto tximport
13 months ago Yijing • 0
1
vote
3
replies
909
views
tximport error
tximport r
updated 13 months ago by 42k • written 13 months ago by • 0
0
votes
2
replies
957
views
combining multiple salmon runs after tximport
tximport RNASeq salmon
updated 15 months ago by ★ 4.2k • written 15 months ago by • 0
1
vote
5
replies
1.2k
views
tximport: kallisto + GENCODE transcript sanitization
tximport
updated 15 months ago by 42k • written 15 months ago by ▴ 90
0
votes
1
reply
764
views
Is it possible to convert transcript-level to gene-level dataset to use it in DESeq2 ?
DESeq2 Transcriptomics tximport deseq txi
updated 16 months ago by ★ 1.5k • written 16 months ago by ▴ 10
0
votes
2
replies
843
views
how to match salmon output to txname
GenomicFeatures tximport salmon
written 16 months ago by • 0
0
votes
1
reply
780
views
Missing transcript
DESeq2 tximport salmon
updated 16 months ago by ★ 4.2k • written 16 months ago by • 0
2
votes
1
reply
721
views
Confused about tximport-DESeq2 setup
DESeq2 tximport salmon
updated 16 months ago by ★ 4.2k • written 16 months ago by • 0
0
votes
2
replies
809
views
Differentially expression analysis of orthologous genes between two species
DESeq2 tximport
18 months ago Konstantinos • 0
2
votes
3
replies
1.3k
views
Error while reading rsem files in tximport
DESeq2 tximport rsem RNASeq tximportData
18 months ago mohammedtoufiq91 ▴ 10
4
votes
3
replies
1.1k
views
tx2gene object trouble when working with kallisto and A.thaliana
tx2gene tximport Arabidopsis_thaliana kallisto
updated 18 months ago by 66k • written 18 months ago by ▴ 10
0
votes
4
replies
2.0k
views
Tximport error message - colnames
tximport
written 3.0 years ago by • 0
0
votes
1
reply
921
views
Trouble with importing transcript counts with Salmon
Salmon tximport RNAseq EdgeR
updated 18 months ago by ★ 4.2k • written 18 months ago by • 0
1
vote
2
replies
815
views
error loading kallisto output in tximport
file.exists false kallisto tximport
18 months ago cta • 0
3
votes
3
replies
973
views
What is the correct way to import transcript abundances from 3' Quantseq results that calculated by kallisto?
tximport tximportData Quantseq kallisto
19 months ago • updated 18 months ago duhwa.lee • 0
2
votes
2
replies
1.3k
views
How to convert transcript counts to gene counts in R?
DESeq2 tximport
19 months ago L ▴ 50
1
vote
2
replies
1.6k
views
transcripts missing from tx2gene
tximport
20 months ago Erick • 0
0
votes
1
reply
655
views
tximport: not all(file.exists(files)) are true
tximport
updated 20 months ago by 42k • written 20 months ago by • 0
3
votes
4
replies
1.3k
views
difference between txi$counts and txi$abundance when countsFromAbundance is true
RNAseq tximport
updated 20 months ago by ★ 4.2k • written 20 months ago by • 0
2
votes
1
reply
1.6k
views
Understanding tximport working with salmon outputs
Transcriptomics tximport
updated 20 months ago by ★ 4.2k • written 20 months ago by ▴ 10
0
votes
3
replies
999
views
tximport error
error tximport
updated 20 months ago by 42k • written 20 months ago by • 0
5
votes
6
replies
1.5k
views
Selecting individual samples from tximport and DGE matrix design with missing biological replicate
DESeq2 limma tximport
updated 20 months ago by 50k • written 21 months ago by • 0
2
votes
8
replies
1.6k
views
RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM tximport scRNAseq DESeq2
23 months ago Kelen ▴ 10
0
votes
4
replies
1.1k
views
Alternative for wininet method in tximeta
DESeq2 tximport tximportData tximeta
23 months ago uhlkatie • 0
1
vote
3
replies
1.7k
views
miRNA differential expression analysis - treat as transcript level?
tximport DESeq2 edgeR swish miRNA
updated 23 months ago by 42k • written 23 months ago by • 0
0
votes
1
reply
1.1k
views
Function Request for Rsubread or tximport: parsing command-line featureCounts output
tximport Rsubread
updated 2.0 years ago by ★ 4.2k • written 2.0 years ago by ▴ 10
50 results • Page 1 of 1
Recent ...
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Comment: Volcano plot of scRNA-seq data not "centered" by ATpoint ★ 4.2k
My comment was generic. If your experiment causes drastic shifts then the situation might be different. The advise is the same: Try to use …
Comment: conumee with Infinium MethylationEPIC v2.0 by Maximus • 0
Hi Sole, If there is a combined mixture of MSet of 450K, EPIC and EPICv2, how should I create an annotation object? I tried to create anno…
Comment: Volcano plot of scRNA-seq data not "centered" by tjl • 0
Thank you both. The code is below, simplified a bit for simplicity. ATpoint, your suggestion re: the top 20% of genes by baseMean makes me …
Comment: Cannot install oligo on Fedora by James W. MacDonald 66k
Wait a minute. The `oligo` package is *supposed to* be using `zlibbioc`, but apparently it is not. I get the same thing as you do, where it…
Comment: Cannot install oligo on Fedora by James W. MacDonald 66k
There is the `zlibbioc` package that provides the headers for zlib 1.2.5, that I think you should be able to use, although that would requi…
Votes
DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Gene symbol
DESeq2 swap ensembl gene id rownames with gene symbol column
A: DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Ge
DESeq2: add annotations (from data frame) to DESeqDataSet
Add new columns to DESeqResults from text file by matching rownames.
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