Showing : tximport • reset
0
votes
11
replies
712
views
Problems with oarfish + tximport + swish
fishpond tximport tximeta
updated 4 weeks ago by • 0 • written 5 weeks ago by • 0
1
vote
2
replies
559
views
Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport DESeq2 GSVA
10 weeks ago • updated 9 weeks ago georgii.vdovin • 0
4
votes
5
replies
757
views
DESeq Input from Salmon + tximport/tximeta
tximportData summarizeToGene tximport DESeq2 salmon
3 months ago LuciaNhu • 0
0
votes
2
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450
views
How can I obtain DEGs that are resulted from using salmon in alignment-based mode or mapping-based mode?
tximport DESeq2
updated 4 months ago by 43k • written 4 months ago by • 0
0
votes
2
replies
473
views
tximport data import
tximport
updated 5 months ago by 43k • written 5 months ago by • 0
1
vote
2
replies
892
views
How to use specific size factors and average transcript lengths from tximport in DESeq2?
DESeq2 tximport
6 months ago grothmn • 0
1
vote
2
replies
2.4k
views
using tximport with STAR transcript-quantification output
tximport deseq2 STAR
updated 8 months ago by ▴ 40 • written 5.3 years ago by • 0
0
votes
4
replies
667
views
Create count matrix from multible quant sf files from different directories
tximportData tximport salmon
8 months ago JG13 • 0
0
votes
2
replies
623
views
edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
10 months ago Marianna ▴ 20
0
votes
2
replies
665
views
Clarification on Library Size Normalization After Using tximport with countsFromAbundance="lengthScaledTPM"
tximport
updated 11 months ago by 43k • written 11 months ago by • 0
2
votes
1
reply
573
views
Creating data matrix in Deseq2 from tximport data invalid class SummarizedExperiment object
DESeq2 tximport
updated 11 months ago by ★ 4.7k • written 11 months ago by • 0
2
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3
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2.7k
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR tximport RNASeq DESeq2
updated 14 months ago by ★ 1.4k • written 14 months ago by • 0
0
votes
1
reply
793
views
tximport error with rsem files
rsem tximport
updated 14 months ago by ★ 4.7k • written 14 months ago by • 0
3
votes
2
replies
1.1k
views
tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
tximport DESeq2
updated 14 months ago by 68k • written 14 months ago by • 0
0
votes
3
replies
912
views
Tximport Error - transcripts in quant files are not the same as tx2gene
salmon tximport deseq2
updated 16 months ago by 43k • written 16 months ago by • 0
10
votes
11
replies
2.9k
views
tximport error: vroom
tximport
updated 16 months ago by • 0 • written 16 months ago by ▴ 40
2
votes
3
replies
1.3k
views
Import Salmon data with tximport and pool technical replicates
tximport edgeR
written 18 months ago by • 0
4
votes
13
replies
3.0k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport DESeq2
updated 17 months ago by 43k • written 18 months ago by • 0
0
votes
4
replies
1.6k
views
Handle zero effective gene length when tximport RSEM results
tximport edgeR
updated 18 months ago by 43k • written 18 months ago by • 0
1
vote
2
replies
2.4k
views
IsoformSwitchAnalyzeR: What are the SV values created in design matrix?
salmon IsoformSwitchAnalyzeR tximport RNASeqData
updated 18 months ago by ▴ 120 • written 19 months ago by ▴ 10
2
votes
9
replies
1.8k
views
Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport tximportData DESeq2
19 months ago Ndimensional ▴ 20
0
votes
2
replies
990
views
tximport error in reading salmon output files?
tximport tximportData
updated 12 months ago by • 0 • written 20 months ago by • 0
0
votes
1
reply
949
views
Which file in tximport should I use for DESeq2 analysis?
tximport DESeq2
updated 21 months ago by 68k • written 21 months ago by • 0
2
votes
1
reply
1.1k
views
scaledTPM for DESeq2 using tximport
DESeq2 tximport
updated 21 months ago by 43k • written 21 months ago by • 0
3
votes
7
replies
1.6k
views
failed to use tximport for creating count matrix from kallisto
tximport kallisto
21 months ago Yijing • 0
0
votes
2
replies
1.3k
views
Error in H5Fopen
rhdf5 Rhdf5lib kallisto tximport
22 months ago Yijing • 0
1
vote
3
replies
1.3k
views
tximport error
tximport r
updated 22 months ago by 43k • written 22 months ago by • 0
0
votes
2
replies
1.4k
views
combining multiple salmon runs after tximport
tximport RNASeq salmon
updated 2.0 years ago by ★ 4.7k • written 2.0 years ago by • 0
1
vote
5
replies
1.7k
views
tximport: kallisto + GENCODE transcript sanitization
tximport
updated 2.0 years ago by 43k • written 2.0 years ago by ▴ 90
6
votes
10
replies
3.0k
views
Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
updated 10 months ago by • 0 • written 2.0 years ago by ▴ 10
0
votes
1
reply
1.0k
views
Is it possible to convert transcript-level to gene-level dataset to use it in DESeq2 ?
DESeq2 Transcriptomics tximport deseq txi
updated 2.1 years ago by ★ 1.6k • written 2.1 years ago by ▴ 10
0
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2
replies
1.3k
views
how to match salmon output to txname
GenomicFeatures tximport salmon
written 2.1 years ago by • 0
0
votes
1
reply
1.2k
views
Missing transcript
DESeq2 tximport salmon
updated 2.1 years ago by ★ 4.7k • written 2.1 years ago by • 0
2
votes
1
reply
1.1k
views
Confused about tximport-DESeq2 setup
DESeq2 tximport salmon
updated 2.1 years ago by ★ 4.7k • written 2.1 years ago by • 0
2
votes
5
replies
2.1k
views
Normalizing Salmon output count data matrix using DESeq2
DESeq2 tximport counts Salmon
updated 12 months ago by 43k • written 2.2 years ago by • 0
0
votes
2
replies
1.1k
views
Differentially expression analysis of orthologous genes between two species
DESeq2 tximport
2.2 years ago Konstantinos • 0
2
votes
3
replies
1.8k
views
Error while reading rsem files in tximport
DESeq2 tximport rsem RNASeq tximportData
2.2 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 2.2 years ago by 68k • written 2.3 years ago by ▴ 10
0
votes
1
reply
1.3k
views
Trouble with importing transcript counts with Salmon
Salmon tximport RNAseq EdgeR
updated 2.3 years ago by ★ 4.7k • written 2.3 years ago by • 0
1
vote
2
replies
1.1k
views
error loading kallisto output in tximport
file.exists false kallisto tximport
2.3 years ago cta • 0
2
votes
3
replies
1.8k
views
How to convert transcript counts to gene counts in R?
DESeq2 tximport
written 2.3 years ago by ▴ 50
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
2.3 years ago duhwa.lee • 0
1
vote
2
replies
2.2k
views
transcripts missing from tx2gene
tximport
2.4 years ago Erick • 0
0
votes
1
reply
935
views
tximport: not all(file.exists(files)) are true
tximport
updated 2.4 years ago by 43k • written 2.4 years ago by • 0
3
votes
1
reply
2.9k
views
Understanding tximport working with salmon outputs
Transcriptomics tximport
updated 2.4 years ago by ★ 4.7k • written 2.4 years ago by ▴ 10
3
votes
4
replies
2.0k
views
difference between txi$counts and txi$abundance when countsFromAbundance is true
RNAseq tximport
updated 2.4 years ago by ★ 4.7k • written 2.4 years ago by • 0
0
votes
3
replies
1.3k
views
tximport error
error tximport
updated 2.4 years ago by 43k • written 2.5 years ago by • 0
5
votes
6
replies
2.1k
views
Selecting individual samples from tximport and DGE matrix design with missing biological replicate
DESeq2 limma tximport
updated 2.4 years ago by 52k • written 2.5 years ago by • 0
0
votes
4
replies
1.5k
views
Alternative for wininet method in tximeta
DESeq2 tximport tximportData tximeta
2.6 years ago uhlkatie • 0
1
vote
3
replies
2.5k
views
miRNA differential expression analysis - treat as transcript level?
tximport DESeq2 edgeR swish miRNA
updated 2.7 years ago by 43k • written 2.7 years ago by • 0
50 results • Page 1 of 1
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Answer: EuroBioC2023 abstract submission is open! by cirwin009 • 0
Submit here https://openreview.net/group?id=bioconductor.org/EuroBioC/2023/ [Block Blast][1] This article offers a thorough and in-depth…
Comment: How to formulate 2 factor nested design in DESeq2 by Mariane • 0
Hi JK Kim, I'm having a problem similar to the one you reported. Could you please tell me how you solved this problem? Thanks
Comment: batch effect removal for agilent microarray data by gaye.yilmaz • 0
Thank you
Answer: Pathview visualisation not including positive log2 fold changes by James W. MacDonald 68k
Without providing a self-contained example, nobody can tell you if/where you went wrong. Since you get a KEGG pathway with some of the gene…
Comment: Differential variance analysis - can i use deseq2 by Marwan • 0
Thanks Michael for your answer, i didnt mean to use Deseq2 directly for the variance testing, but more like asking if using the (VST) data…
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Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Suggesting changing the "reply-to" field to the mailing list address.
Answer: UniProt.ws query for single UniRef90 ID takes several minutes
A: How to extract DESeq2 results for an interaction design
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
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