Showing : tximport • reset
6
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10
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1.7k
views
Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
updated 4 weeks ago by • 0 • written 15 months ago by ▴ 10
0
votes
2
replies
198
views
edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
6 weeks ago Marianna ▴ 20
0
votes
2
replies
216
views
Clarification on Library Size Normalization After Using tximport with countsFromAbundance="lengthScaledTPM"
tximport
updated 7 weeks ago by 42k • written 7 weeks ago by • 0
0
votes
5
replies
9.3k
views
tximport all(file.exists(files)) is not TRUE
bioconductor tximport rnaseq R
updated 8 weeks ago by • 0 • written 7.6 years ago by • 0
2
votes
1
reply
272
views
Creating data matrix in Deseq2 from tximport data invalid class SummarizedExperiment object
DESeq2 tximport
updated 9 weeks ago by ★ 4.1k • written 9 weeks ago by • 0
2
votes
5
replies
1.4k
views
Normalizing Salmon output count data matrix using DESeq2
DESeq2 tximport counts Salmon
updated 12 weeks ago by 42k • written 17 months ago by • 0
0
votes
2
replies
685
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 4 months ago by ★ 1.4k • written 5 months ago by • 0
0
votes
1
reply
368
views
tximport error with rsem files
rsem tximport
updated 5 months ago by ★ 4.1k • written 5 months ago by • 0
3
votes
2
replies
586
views
tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
tximport DESeq2
updated 5 months ago by 65k • written 5 months ago by • 0
10
votes
11
replies
2.0k
views
tximport error: vroom
tximport
updated 6 months ago by • 0 • written 7 months ago by ▴ 40
0
votes
3
replies
452
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
1.4k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport DESeq2
updated 7 months ago by 42k • written 8 months ago by • 0
2
votes
3
replies
842
views
Import Salmon data with tximport and pool technical replicates
tximport edgeR
written 9 months ago by • 0
0
votes
4
replies
921
views
Handle zero effective gene length when tximport RSEM results
tximport edgeR
updated 8 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 9 months ago by ▴ 120 • written 9 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
2.8k
views
tximport error: all(txId == raw[[txIdCol]]) is not TRUE
tximport
updated 10 months ago by 42k • written 2.5 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
1.2k
views
tximport importer isoform abundance
tximport
updated 12 months ago by ▴ 190 • written 3.9 years ago by ▴ 620
0
votes
1
reply
641
views
Which file in tximport should I use for DESeq2 analysis?
tximport DESeq2
updated 12 months ago by 65k • written 12 months ago by • 0
2
votes
1
reply
677
views
scaledTPM for DESeq2 using tximport
DESeq2 tximport
updated 12 months ago by 42k • written 12 months ago by • 0
3
votes
7
replies
1.1k
views
failed to use tximport for creating count matrix from kallisto
tximport kallisto
12 months ago Yijing • 0
0
votes
2
replies
851
views
Error in H5Fopen
rhdf5 Rhdf5lib kallisto tximport
12 months ago Yijing • 0
1
vote
3
replies
890
views
tximport error
tximport r
updated 13 months ago by 42k • written 13 months ago by • 0
0
votes
2
replies
946
views
combining multiple salmon runs after tximport
tximport RNASeq salmon
updated 15 months ago by ★ 4.1k • 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
751
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
824
views
how to match salmon output to txname
GenomicFeatures tximport salmon
written 16 months ago by • 0
0
votes
1
reply
767
views
Missing transcript
DESeq2 tximport salmon
updated 16 months ago by ★ 4.1k • written 16 months ago by • 0
2
votes
1
reply
707
views
Confused about tximport-DESeq2 setup
DESeq2 tximport salmon
updated 16 months ago by ★ 4.1k • written 16 months ago by • 0
0
votes
2
replies
802
views
Differentially expression analysis of orthologous genes between two species
DESeq2 tximport
17 months ago Konstantinos • 0
2
votes
3
replies
1.3k
views
Error while reading rsem files in tximport
DESeq2 tximport rsem RNASeq tximportData
17 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 65k • written 18 months ago by ▴ 10
0
votes
4
replies
2.0k
views
Tximport error message - colnames
tximport
written 2.9 years ago by • 0
0
votes
1
reply
914
views
Trouble with importing transcript counts with Salmon
Salmon tximport RNAseq EdgeR
updated 18 months ago by ★ 4.1k • written 18 months ago by • 0
1
vote
2
replies
811
views
error loading kallisto output in tximport
file.exists false kallisto tximport
18 months ago cta • 0
3
votes
3
replies
961
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
649
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 ★ 4.1k • 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 ★ 4.1k • written 20 months ago by ▴ 10
0
votes
3
replies
992
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 20 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 • updated 22 months ago Kelen ▴ 10
0
votes
4
replies
1.1k
views
Alternative for wininet method in tximeta
DESeq2 tximport tximportData tximeta
22 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
1.0k
views
Function Request for Rsubread or tximport: parsing command-line featureCounts output
tximport Rsubread
updated 2.0 years ago by ★ 4.1k • written 2.0 years ago by ▴ 10
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Comment: all variables in design formula must be columns in colData (Deseq2) error by Galina • 0
thank you!
Comment: all variables in design formula must be columns in colData (Deseq2) error by ATpoint ★ 4.1k
coldata_rat <- data.frame(conditions=..., batch=...)
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by robersy • 0
Thank you all for your comments. I will follow your suggestions.
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by Ken C • 0
Hi Michael, thanks a lot for your prompt reply! Not sure if this is appropriate or if you are the right person to ask -- is there anything…
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by Ken C • 0
Well, if I look at genes with baseMean>50, then the relative absolute difference in log2FoldChange (say over the absolute log2FoldChange of…
Votes
biomaRt not working - lazy table error
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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