Showing : txImport • reset
0
votes
11
replies
747
views
Problems with oarfish + tximport + swish
fishpond tximport tximeta
updated 6 weeks ago by • 0 • written 6 weeks ago by • 0
1
vote
2
replies
601
views
Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport DESeq2 GSVA
11 weeks ago georgii.vdovin • 0
4
votes
5
replies
794
views
DESeq Input from Salmon + tximport/tximeta
tximportData summarizeToGene tximport DESeq2 salmon
3 months ago LuciaNhu • 0
0
votes
2
replies
469
views
How can I obtain DEGs that are resulted from using salmon in alignment-based mode or mapping-based mode?
tximport DESeq2
updated 5 months ago by 43k • written 5 months ago by • 0
0
votes
2
replies
480
views
tximport data import
tximport
updated 5 months ago by 43k • written 6 months ago by • 0
1
vote
2
replies
915
views
How to use specific size factors and average transcript lengths from tximport in DESeq2?
DESeq2 tximport
7 months ago grothmn • 0
1
vote
2
replies
2.4k
views
using tximport with STAR transcript-quantification output
tximport deseq2 STAR
updated 9 months ago by ▴ 40 • written 5.3 years ago by • 0
0
votes
4
replies
687
views
Create count matrix from multible quant sf files from different directories
tximportData tximport salmon
9 months ago JG13 • 0
0
votes
2
replies
641
views
edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
11 months ago Marianna ▴ 20
0
votes
2
replies
690
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
586
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
votes
3
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2.8k
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
813
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 15 months ago by 68k • written 15 months ago by • 0
0
votes
3
replies
938
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 17 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
3.1k
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 19 months ago by ▴ 120 • written 19 months ago by ▴ 10
2
votes
9
replies
1.9k
views
Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport tximportData DESeq2
20 months ago Ndimensional ▴ 20
0
votes
2
replies
1.0k
views
tximport error in reading salmon output files?
tximport tximportData
updated 13 months ago by • 0 • written 20 months ago by • 0
0
votes
1
reply
962
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 22 months ago by 43k • written 22 months ago by • 0
3
votes
7
replies
1.6k
views
failed to use tximport for creating count matrix from kallisto
tximport kallisto
22 months ago Yijing • 0
0
votes
2
replies
1.4k
views
Error in H5Fopen
rhdf5 Rhdf5lib kallisto tximport
22 months ago Yijing • 0
1
vote
3
replies
1.4k
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
3.1k
views
Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
updated 10 months ago by • 0 • written 2.1 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
votes
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 2.2 years ago by ★ 4.7k • written 2.2 years ago by • 0
2
votes
1
reply
1.1k
views
Confused about tximport-DESeq2 setup
DESeq2 tximport salmon
updated 2.2 years ago by ★ 4.7k • written 2.2 years ago by • 0
2
votes
5
replies
2.2k
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
1.2k
views
Differentially expression analysis of orthologous genes between two species
DESeq2 tximport
2.3 years ago Konstantinos • 0
2
votes
3
replies
1.8k
views
Error while reading rsem files in tximport
DESeq2 tximport rsem RNASeq tximportData
2.3 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 2.3 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
1.9k
views
How to convert transcript counts to gene counts in R?
DESeq2 tximport
written 2.4 years ago by ▴ 50
3
votes
3
replies
1.5k
views
What is the correct way to import transcript abundances from 3' Quantseq results that calculated by kallisto?
tximport tximportData Quantseq kallisto
2.4 years ago • updated 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
945
views
tximport: not all(file.exists(files)) are true
tximport
updated 2.5 years ago by 43k • written 2.5 years ago by • 0
3
votes
1
reply
3.0k
views
Understanding tximport working with salmon outputs
Transcriptomics tximport
updated 2.5 years ago by ★ 4.7k • written 2.5 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 2.5 years ago by ★ 4.7k • written 2.5 years ago by • 0
0
votes
3
replies
1.3k
views
tximport error
error tximport
updated 2.5 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 2.5 years ago by 52k • written 2.5 years ago by • 0
0
votes
4
replies
1.6k
views
Alternative for wininet method in tximeta
DESeq2 tximport tximportData tximeta
2.7 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
Recent ...
Replies
Comment: how many significant figures are there in DESeq2 output by ATpoint ★ 4.7k
If you want consistency then use a fixed software environment like Docker, wirh fixed code and thresholds that make sense. Rounding to near…
Comment: Compare TCGA-PAAD with GTEx gene expression by Jane • 0
why aren't there any answers?
Comment: Too many significant genes when integrating gtex and tcga by Jane • 0
I encountered the same issue: too many DEGs after limma analysis. It is sad that until today we can still see the paper published where GTE…
Comment: how many significant figures are there in DESeq2 output by Matthew McCormack ▴ 180
Thank you for your reply. It is good to know that cutoff of 0.05 means less than 0.05. My concerns are about consistency and reproducibili…
Comment: DiffBind edgeR normalization --- why are the normalization factors all equal to by ATpoint ★ 4.7k
No, normalization factors from edgeR rather than size factors from DESeq2 are not proportional, it's a different concept and implementation…
Votes
A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct
Answer: Group-specific condition effects with individuals nested: matrix is not full ra
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