Showing : Tximport • reset
6
votes
7
replies
3.2k
views
edgeR + tximport: calcNormFactors and the usage of offsets
edgeR tximport differential expression
updated 14 days ago by 52k • written 4.7 years ago by ▴ 20
1
vote
2
replies
470
views
Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport DESeq2 GSVA
4 weeks ago georgii.vdovin • 0
4
votes
5
replies
672
views
DESeq Input from Salmon + tximport/tximeta
tximportData summarizeToGene tximport DESeq2 salmon
10 weeks ago • updated 9 weeks ago LuciaNhu • 0
0
votes
2
replies
407
views
How can I obtain DEGs that are resulted from using salmon in alignment-based mode or mapping-based mode?
tximport DESeq2
updated 3 months ago by 43k • written 3 months ago by • 0
0
votes
2
replies
439
views
tximport data import
tximport
updated 4 months ago by 43k • written 4 months ago by • 0
1
vote
2
replies
820
views
How to use specific size factors and average transcript lengths from tximport in DESeq2?
DESeq2 tximport
5 months ago grothmn • 0
1
vote
2
replies
2.3k
views
using tximport with STAR transcript-quantification output
tximport deseq2 STAR
updated 7 months ago by ▴ 40 • written 5.2 years ago by • 0
0
votes
4
replies
623
views
Create count matrix from multible quant sf files from different directories
tximportData tximport salmon
7 months ago JG13 • 0
2
votes
3
replies
1.8k
views
How to convert transcript counts to gene counts in R?
DESeq2 tximport
written 2.2 years ago by ▴ 50
6
votes
10
replies
2.8k
views
Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
updated 8 months ago by • 0 • written 23 months ago by ▴ 10
0
votes
2
replies
576
views
edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
9 months ago Marianna ▴ 20
0
votes
2
replies
613
views
Clarification on Library Size Normalization After Using tximport with countsFromAbundance="lengthScaledTPM"
tximport
updated 9 months ago by 43k • written 9 months ago by • 0
0
votes
5
replies
10k
views
tximport all(file.exists(files)) is not TRUE
bioconductor tximport rnaseq R
updated 10 months ago by • 0 • written 8.3 years ago by • 0
2
votes
1
reply
527
views
Creating data matrix in Deseq2 from tximport data invalid class SummarizedExperiment object
DESeq2 tximport
updated 10 months ago by ★ 4.6k • written 10 months ago by • 0
2
votes
5
replies
2.0k
views
Normalizing Salmon output count data matrix using DESeq2
DESeq2 tximport counts Salmon
updated 10 months ago by 43k • written 2.1 years ago by • 0
0
votes
2
replies
947
views
tximport error in reading salmon output files?
tximport tximportData
updated 11 months ago by • 0 • written 19 months ago by • 0
2
votes
3
replies
2.5k
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR tximport RNASeq DESeq2
updated 12 months ago by ★ 1.4k • written 13 months ago by • 0
0
votes
1
reply
733
views
tximport error with rsem files
rsem tximport
updated 13 months ago by ★ 4.6k • written 13 months ago by • 0
3
votes
2
replies
1.0k
views
tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
tximport DESeq2
updated 13 months ago by 67k • written 13 months ago by • 0
10
votes
11
replies
2.8k
views
tximport error: vroom
tximport
updated 14 months ago by • 0 • written 15 months ago by ▴ 40
0
votes
3
replies
835
views
Tximport Error - transcripts in quant files are not the same as tx2gene
salmon tximport deseq2
updated 15 months ago by 43k • written 15 months ago by • 0
4
votes
13
replies
2.8k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport DESeq2
updated 15 months ago by 43k • written 16 months ago by • 0
2
votes
3
replies
1.2k
views
Import Salmon data with tximport and pool technical replicates
tximport edgeR
written 17 months ago by • 0
0
votes
4
replies
1.5k
views
Handle zero effective gene length when tximport RSEM results
tximport edgeR
updated 16 months ago by 43k • written 17 months ago by • 0
1
vote
2
replies
2.3k
views
IsoformSwitchAnalyzeR: What are the SV values created in design matrix?
salmon IsoformSwitchAnalyzeR tximport RNASeqData
updated 17 months ago by ▴ 120 • written 17 months ago by ▴ 10
16
votes
25
replies
3.8k
views
dtuScaledTPM vs lengthScaledTPM in DTU analysis
tximport dtu salmon TPM rnaseqDTU
written 5.8 years ago by ▴ 60
1
vote
5
replies
3.5k
views
tximport error: all(txId == raw[[txIdCol]]) is not TRUE
tximport
updated 18 months ago by 43k • written 3.2 years ago by • 0
2
votes
9
replies
1.8k
views
Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport tximportData DESeq2
18 months ago Ndimensional ▴ 20
4
votes
9
replies
5.0k
views
How to get DESeq2 sizefactors from data imported using tximport
deseq2 sailfish tximport
updated 20 months ago by • 0 • written 7.5 years ago by • 0
0
votes
4
replies
1.5k
views
tximport importer isoform abundance
tximport
updated 20 months ago by ▴ 200 • written 4.6 years ago by ▴ 620
0
votes
1
reply
921
views
Which file in tximport should I use for DESeq2 analysis?
tximport DESeq2
updated 20 months ago by 67k • written 20 months ago by • 0
2
votes
1
reply
1.0k
views
scaledTPM for DESeq2 using tximport
DESeq2 tximport
updated 20 months ago by 43k • written 20 months ago by • 0
3
votes
7
replies
1.6k
views
failed to use tximport for creating count matrix from kallisto
tximport kallisto
20 months ago Yijing • 0
0
votes
2
replies
1.3k
views
Error in H5Fopen
rhdf5 Rhdf5lib kallisto tximport
20 months ago Yijing • 0
1
vote
3
replies
1.3k
views
tximport error
tximport r
updated 21 months ago by 43k • written 21 months ago by • 0
0
votes
2
replies
1.3k
views
combining multiple salmon runs after tximport
tximport RNASeq salmon
updated 23 months ago by ★ 4.6k • written 23 months ago by • 0
1
vote
5
replies
1.7k
views
tximport: kallisto + GENCODE transcript sanitization
tximport
updated 23 months ago by 43k • written 23 months ago by ▴ 90
0
votes
1
reply
983
views
Is it possible to convert transcript-level to gene-level dataset to use it in DESeq2 ?
DESeq2 Transcriptomics tximport deseq txi
updated 24 months ago by ★ 1.5k • written 24 months ago by ▴ 10
0
votes
2
replies
1.2k
views
how to match salmon output to txname
GenomicFeatures tximport salmon
written 2.0 years ago by • 0
0
votes
1
reply
1.1k
views
Missing transcript
DESeq2 tximport salmon
updated 2.0 years ago by ★ 4.6k • written 2.0 years ago by • 0
2
votes
1
reply
1.0k
views
Confused about tximport-DESeq2 setup
DESeq2 tximport salmon
updated 2.0 years ago by ★ 4.6k • written 2.0 years ago by • 0
0
votes
2
replies
1.1k
views
Differentially expression analysis of orthologous genes between two species
DESeq2 tximport
2.1 years ago Konstantinos • 0
2
votes
3
replies
1.7k
views
Error while reading rsem files in tximport
DESeq2 tximport rsem RNASeq tximportData
2.1 years ago mohammedtoufiq91 ▴ 10
4
votes
3
replies
1.5k
views
tx2gene object trouble when working with kallisto and A.thaliana
tx2gene tximport Arabidopsis_thaliana kallisto
updated 2.1 years ago by 67k • written 2.2 years ago by ▴ 10
0
votes
4
replies
2.4k
views
Tximport error message - colnames
tximport
written 3.6 years ago by • 0
0
votes
1
reply
1.2k
views
Trouble with importing transcript counts with Salmon
Salmon tximport RNAseq EdgeR
updated 2.2 years ago by ★ 4.6k • written 2.2 years ago by • 0
1
vote
2
replies
1.1k
views
error loading kallisto output in tximport
file.exists false kallisto tximport
2.2 years ago cta • 0
3
votes
3
replies
1.4k
views
What is the correct way to import transcript abundances from 3' Quantseq results that calculated by kallisto?
tximport tximportData Quantseq kallisto
2.2 years ago duhwa.lee • 0
1
vote
2
replies
2.1k
views
transcripts missing from tx2gene
tximport
2.3 years ago Erick • 0
0
votes
1
reply
905
views
tximport: not all(file.exists(files)) are true
tximport
updated 2.3 years ago by 43k • written 2.3 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: promoters_txdb <- promoters(txdb, upstream = 2000) is not 2000 by James W. MacDonald 67k
If you use `promoters` and do not provide an argument for something that has a default, you will get the default argument. Your last call t…
Comment: org.Hs.eg.db issue by k.panov • 0
installed R on another PC, works perfectly. ergo, problem outside of R probably..... :-(
Comment: MBDseq analysis using qsea package by Lukas ▴ 20
Hi, I checked in with Matthias and here is his response: You need to indicate "samples": "The indices of the samples for which individu…
Comment: DESeq2 analysis with transcript counts by sindhuri • 0
Thank you for the response. Currently I am using the R studio for analysis and Im running DESeq2 for analysis of the **transcript counts.ts…
Comment: iam not able to do retrive data using GEOquery R package by James W. MacDonald 67k
Another alternative is to use the `GEOmetadb` package ([vignette here)][1], which will allow you to make queries to identify GEO datasets t…
Votes
A: Linear regression in DESeq2
Answer: Is there any chance to solve "the model matrix is not full rank" in DESeq2?
Answer: Issue carrying out DiffBind Analysis at a predefined peak set
Answer: Differential variability modelling with vst() expression
Answer: Differential variability modelling with vst() expression
Awards • All
Popular Question to Gordon Smyth 52k
Popular Question to linouhao ▴ 20
Popular Question to spg • 0
Popular Question to otieno43 • 0
Popular Question to svlachavas ▴ 840
Locations • All
United States, 18 minutes ago
Germany/Heidelberg/German Cancer Research Center, 21 minutes ago
UPF, Barcelona, Spain, 25 minutes ago
Kazakhstan, 31 minutes ago
WEHI, Melbourne, Australia, 41 minutes ago
Traffic: 807 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