Showing : Tximport • reset
6
votes
10
replies
1.6k
views
Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
updated 16 days ago by • 0 • written 15 months ago by ▴ 10
0
votes
2
replies
168
views
edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
4 weeks ago Marianna ▴ 20
0
votes
2
replies
208
views
Clarification on Library Size Normalization After Using tximport with countsFromAbundance="lengthScaledTPM"
tximport
updated 5 weeks ago by 41k • written 5 weeks ago by • 0
0
votes
5
replies
9.3k
views
tximport all(file.exists(files)) is not TRUE
bioconductor tximport rnaseq R
updated 6 weeks ago by • 0 • written 7.6 years ago by • 0
2
votes
1
reply
248
views
Creating data matrix in Deseq2 from tximport data invalid class SummarizedExperiment object
DESeq2 tximport
updated 7 weeks ago by ★ 4.1k • written 7 weeks ago by • 0
2
votes
5
replies
1.4k
views
Normalizing Salmon output count data matrix using DESeq2
DESeq2 tximport counts Salmon
updated 10 weeks ago by 41k • written 16 months ago by • 0
0
votes
2
replies
665
views
tximport error in reading salmon output files?
tximport tximportData
updated 3 months ago by • 0 • written 10 months ago by • 0
2
votes
3
replies
1.2k
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 ★ 1.3k • written 4 months ago by • 0
0
votes
1
reply
353
views
tximport error with rsem files
rsem tximport
updated 4 months ago by ★ 4.1k • written 4 months ago by • 0
3
votes
2
replies
562
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
1.9k
views
tximport error: vroom
tximport
updated 6 months ago by • 0 • written 7 months ago by ▴ 40
0
votes
3
replies
429
views
Tximport Error - transcripts in quant files are not the same as tx2gene
salmon tximport deseq2
updated 6 months ago by 41k • written 6 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 41k • written 8 months ago by • 0
2
votes
3
replies
814
views
Import Salmon data with tximport and pool technical replicates
tximport edgeR
written 8 months ago by • 0
0
votes
4
replies
885
views
Handle zero effective gene length when tximport RSEM results
tximport edgeR
updated 8 months ago by 41k • written 8 months ago by • 0
1
vote
2
replies
1.5k
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
3.0k
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 9 months ago by 41k • 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 11 months ago by • 0 • written 6.8 years ago by • 0
0
votes
4
replies
1.2k
views
tximport importer isoform abundance
tximport
updated 11 months ago by ▴ 190 • written 3.9 years ago by ▴ 620
0
votes
1
reply
615
views
Which file in tximport should I use for DESeq2 analysis?
tximport DESeq2
updated 11 months ago by 65k • written 11 months ago by • 0
2
votes
1
reply
656
views
scaledTPM for DESeq2 using tximport
DESeq2 tximport
updated 12 months ago by 41k • 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
826
views
Error in H5Fopen
rhdf5 Rhdf5lib kallisto tximport
12 months ago Yijing • 0
1
vote
3
replies
871
views
tximport error
tximport r
updated 12 months ago by 41k • written 12 months ago by • 0
0
votes
2
replies
922
views
combining multiple salmon runs after tximport
tximport RNASeq salmon
updated 14 months ago by ★ 4.1k • written 14 months ago by • 0
1
vote
5
replies
1.2k
views
tximport: kallisto + GENCODE transcript sanitization
tximport
updated 14 months ago by 41k • written 14 months ago by ▴ 90
0
votes
1
reply
730
views
Is it possible to convert transcript-level to gene-level dataset to use it in DESeq2 ?
DESeq2 Transcriptomics tximport deseq txi
updated 15 months ago by ★ 1.5k • written 15 months ago by ▴ 10
0
votes
2
replies
802
views
how to match salmon output to txname
GenomicFeatures tximport salmon
written 16 months ago by • 0
0
votes
1
reply
742
views
Missing transcript
DESeq2 tximport salmon
updated 16 months ago by ★ 4.1k • written 16 months ago by • 0
2
votes
1
reply
687
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
785
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 17 months ago by 65k • written 17 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
897
views
Trouble with importing transcript counts with Salmon
Salmon tximport RNAseq EdgeR
updated 17 months ago by ★ 4.1k • written 17 months ago by • 0
1
vote
2
replies
797
views
error loading kallisto output in tximport
file.exists false kallisto tximport
18 months ago cta • 0
3
votes
3
replies
936
views
What is the correct way to import transcript abundances from 3' Quantseq results that calculated by kallisto?
tximport tximportData Quantseq kallisto
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
18 months ago L ▴ 50
1
vote
2
replies
1.5k
views
transcripts missing from tx2gene
tximport
19 months ago Erick • 0
0
votes
1
reply
632
views
tximport: not all(file.exists(files)) are true
tximport
updated 19 months ago by 41k • written 19 months ago by • 0
3
votes
4
replies
1.2k
views
difference between txi$counts and txi$abundance when countsFromAbundance is true
RNAseq tximport
updated 19 months ago by ★ 4.1k • written 20 months ago by • 0
2
votes
1
reply
1.5k
views
Understanding tximport working with salmon outputs
Transcriptomics tximport
updated 19 months ago by ★ 4.1k • written 19 months ago by ▴ 10
0
votes
3
replies
978
views
tximport error
error tximport
updated 20 months ago by 41k • 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
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 22 months ago by 41k • written 22 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 23 months ago by ★ 4.1k • written 23 months ago by ▴ 10
50 results • Page 1 of 1
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Replies
Answer: Method to find pathways different between 2 groups by Gordon Smyth 50k
> When I search camera limma on pubmed, I found 2 papers I am unclear what point you are trying to make. limma's camera method has been fo…
Comment: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
limma most certainly is available. It installs in R 4.4.0 and Bioc 3.19 for all platforms without any issues. It has not had any period of …
Comment: package goseq seems to be not available on the latest version of R by Patrycja ▴ 20
limma package also isn't available.Is there any information when these packages will be available?
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 41k
Check the number of bootstrapped data per chromosome compared to the original, and then you can also look at its distribution. For this it'…
Comment: DNAString: Standard checksum function? by Henrik Bengtsson ★ 2.4k
For completeness: SEGUID v2 (https://www.seguid.org/), implemented in CRAN package **[seguid](https://cran.r-project.org/package=seguid)*…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Handling multiple differential expression comparisons
Answer: fgsea significant result
Answer: fgsea significant result
package goseq seems to be not available on the latest version of R
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