Showing : tximport • reset
4
votes
5
replies
532
views
DESeq Input from Salmon + tximport/tximeta
tximportData summarizeToGene tximport DESeq2 salmon
10 days ago • updated 9 days ago LuciaNhu • 0
0
votes
2
replies
333
views
How can I obtain DEGs that are resulted from using salmon in alignment-based mode or mapping-based mode?
tximport DESeq2
updated 6 weeks ago by 42k • written 6 weeks ago by • 0
0
votes
2
replies
387
views
tximport data import
tximport
updated 10 weeks ago by 42k • written 10 weeks ago by • 0
1
vote
2
replies
730
views
How to use specific size factors and average transcript lengths from tximport in DESeq2?
DESeq2 tximport
3 months ago grothmn • 0
1
vote
2
replies
2.2k
views
using tximport with STAR transcript-quantification output
tximport deseq2 STAR
updated 5 months ago by ▴ 40 • written 5.0 years ago by • 0
0
votes
4
replies
560
views
Create count matrix from multible quant sf files from different directories
tximportData tximport salmon
5 months ago JG13 • 0
0
votes
2
replies
501
views
edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
7 months ago Marianna ▴ 20
0
votes
2
replies
523
views
Clarification on Library Size Normalization After Using tximport with countsFromAbundance="lengthScaledTPM"
tximport
updated 7 months ago by 42k • written 7 months ago by • 0
2
votes
1
reply
469
views
Creating data matrix in Deseq2 from tximport data invalid class SummarizedExperiment object
DESeq2 tximport
updated 8 months ago by ★ 4.5k • written 8 months ago by • 0
2
votes
3
replies
2.3k
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR tximport RNASeq DESeq2
updated 10 months ago by ★ 1.4k • written 11 months ago by • 0
0
votes
1
reply
653
views
tximport error with rsem files
rsem tximport
updated 11 months ago by ★ 4.5k • written 11 months ago by • 0
3
votes
2
replies
933
views
tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
tximport DESeq2
updated 11 months ago by 67k • written 11 months ago by • 0
0
votes
3
replies
752
views
Tximport Error - transcripts in quant files are not the same as tx2gene
salmon tximport deseq2
updated 13 months ago by 42k • written 13 months ago by • 0
10
votes
11
replies
2.7k
views
tximport error: vroom
tximport
updated 12 months ago by • 0 • written 13 months ago by ▴ 40
2
votes
3
replies
1.1k
views
Import Salmon data with tximport and pool technical replicates
tximport edgeR
written 15 months ago by • 0
4
votes
13
replies
2.5k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport DESeq2
updated 13 months ago by 42k • written 14 months ago by • 0
0
votes
4
replies
1.4k
views
Handle zero effective gene length when tximport RSEM results
tximport edgeR
updated 14 months ago by 42k • written 15 months ago by • 0
1
vote
2
replies
2.2k
views
IsoformSwitchAnalyzeR: What are the SV values created in design matrix?
salmon IsoformSwitchAnalyzeR tximport RNASeqData
updated 15 months ago by ▴ 120 • written 15 months ago by ▴ 10
2
votes
9
replies
1.7k
views
Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport tximportData DESeq2
16 months ago Ndimensional ▴ 20
0
votes
2
replies
898
views
tximport error in reading salmon output files?
tximport tximportData
updated 9 months ago by • 0 • written 17 months ago by • 0
0
votes
1
reply
879
views
Which file in tximport should I use for DESeq2 analysis?
tximport DESeq2
updated 18 months ago by 67k • written 18 months ago by • 0
2
votes
1
reply
966
views
scaledTPM for DESeq2 using tximport
DESeq2 tximport
updated 18 months ago by 42k • written 18 months ago by • 0
3
votes
7
replies
1.5k
views
failed to use tximport for creating count matrix from kallisto
tximport kallisto
18 months ago Yijing • 0
0
votes
2
replies
1.2k
views
Error in H5Fopen
rhdf5 Rhdf5lib kallisto tximport
18 months ago Yijing • 0
1
vote
3
replies
1.2k
views
tximport error
tximport r
updated 19 months ago by 42k • written 19 months ago by • 0
0
votes
2
replies
1.2k
views
combining multiple salmon runs after tximport
tximport RNASeq salmon
updated 21 months ago by ★ 4.5k • written 21 months ago by • 0
1
vote
5
replies
1.6k
views
tximport: kallisto + GENCODE transcript sanitization
tximport
updated 21 months ago by 42k • written 21 months ago by ▴ 90
6
votes
10
replies
2.6k
views
Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
updated 6 months ago by • 0 • written 21 months ago by ▴ 10
0
votes
1
reply
941
views
Is it possible to convert transcript-level to gene-level dataset to use it in DESeq2 ?
DESeq2 Transcriptomics tximport deseq txi
updated 22 months ago by ★ 1.5k • written 22 months ago by ▴ 10
0
votes
2
replies
1.1k
views
how to match salmon output to txname
GenomicFeatures tximport salmon
written 22 months ago by • 0
0
votes
1
reply
1.0k
views
Missing transcript
DESeq2 tximport salmon
updated 22 months ago by ★ 4.5k • written 22 months ago by • 0
2
votes
1
reply
960
views
Confused about tximport-DESeq2 setup
DESeq2 tximport salmon
updated 22 months ago by ★ 4.5k • written 22 months ago by • 0
2
votes
5
replies
1.8k
views
Normalizing Salmon output count data matrix using DESeq2
DESeq2 tximport counts Salmon
updated 8 months ago by 42k • written 22 months ago by • 0
0
votes
2
replies
1.0k
views
Differentially expression analysis of orthologous genes between two species
DESeq2 tximport
23 months ago Konstantinos • 0
2
votes
3
replies
1.6k
views
Error while reading rsem files in tximport
DESeq2 tximport rsem RNASeq tximportData
23 months ago mohammedtoufiq91 ▴ 10
4
votes
3
replies
1.4k
views
tx2gene object trouble when working with kallisto and A.thaliana
tx2gene tximport Arabidopsis_thaliana kallisto
updated 24 months ago by 67k • written 24 months ago by ▴ 10
0
votes
1
reply
1.1k
views
Trouble with importing transcript counts with Salmon
Salmon tximport RNAseq EdgeR
updated 24 months ago by ★ 4.5k • written 24 months ago by • 0
1
vote
2
replies
1.0k
views
error loading kallisto output in tximport
file.exists false kallisto tximport
2.0 years ago cta • 0
2
votes
3
replies
1.7k
views
How to convert transcript counts to gene counts in R?
DESeq2 tximport
written 2.1 years ago by ▴ 50
3
votes
3
replies
1.3k
views
What is the correct way to import transcript abundances from 3' Quantseq results that calculated by kallisto?
tximport tximportData Quantseq kallisto
2.1 years ago • updated 2.0 years ago duhwa.lee • 0
1
vote
2
replies
2.0k
views
transcripts missing from tx2gene
tximport
2.2 years ago • updated 2.1 years ago Erick • 0
0
votes
1
reply
859
views
tximport: not all(file.exists(files)) are true
tximport
updated 2.2 years ago by 42k • written 2.2 years ago by • 0
2
votes
1
reply
2.4k
views
Understanding tximport working with salmon outputs
Transcriptomics tximport
updated 2.2 years ago by ★ 4.5k • written 2.2 years ago by ▴ 10
3
votes
4
replies
1.8k
views
difference between txi$counts and txi$abundance when countsFromAbundance is true
RNAseq tximport
updated 2.2 years ago by ★ 4.5k • written 2.2 years ago by • 0
0
votes
3
replies
1.2k
views
tximport error
error tximport
updated 2.2 years ago by 42k • written 2.2 years ago by • 0
5
votes
6
replies
1.9k
views
Selecting individual samples from tximport and DGE matrix design with missing biological replicate
DESeq2 limma tximport
updated 2.2 years ago by 51k • written 2.2 years ago by • 0
0
votes
4
replies
1.4k
views
Alternative for wininet method in tximeta
DESeq2 tximport tximportData tximeta
2.4 years ago uhlkatie • 0
1
vote
3
replies
2.2k
views
miRNA differential expression analysis - treat as transcript level?
tximport DESeq2 edgeR swish miRNA
updated 2.4 years ago by 42k • written 2.4 years ago by • 0
2
votes
8
replies
2.0k
views
RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM tximport scRNAseq DESeq2
2.4 years ago Kelen ▴ 10
0
votes
1
reply
1.3k
views
Function Request for Rsubread or tximport: parsing command-line featureCounts output
tximport Rsubread
updated 2.5 years ago by ★ 4.5k • written 2.5 years ago by ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Answer: [How to construct a model.matrix ] by Gordon Smyth 51k
> Initially, I simply used > `lm(Epigenetic_age ~ Age_group + Age + Sex + PC1 + PC2 + PC3 + PC4 + PC5 + B + CD4T + CD8T + Mono + NK + Neutr…
Comment: How to extract phastcons score for all protein coding genes and lncRNAs using Ge by rania.alanany • 0
Hi Robert, Thank you for the explanation, But I am still little bit confused, Is the annotation package (TxDb.Hsapiens.UCSC.hg38.knownGene)…
Comment: Merge Replicates vs Mixed Model by abadgerw • 0
@gabrielhoffman any insight?
Comment: makeContrastsDream for Interaction by abadgerw • 0
@gabrielhoffman any insight?
Comment: ColData and ERROR: rows did not converge in beta, labelled in mcols(object)$beta by Michael Love 42k
That is the rows that did converge.
Votes
A: Some questions for remove batch effect by using mnnCorrect
A: Recommendations for combining multiple 10x runs into one SingleCellExperiment
Answer: [How to construct a model.matrix ]
Answer: Handling biological replicates in DESeq2
Comment: biomaRt rnorvegicus_gene_ensembl not available anymore
Awards • All
Popular Question to Michael Stadler ▴ 350
Scholar to ATpoint ★ 4.5k
Commentator to James W. MacDonald 67k
Popular Question to Stefano Mangiola ▴ 20
Popular Question to Shian Su ▴ 40
Locations • All
France, 12 minutes ago
Japan, 24 minutes ago
The city by the bay, 39 minutes ago
United States, 41 minutes ago
WEHI, Melbourne, Australia, 47 minutes ago
Traffic: 602 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6