Showing : Tximport • reset
0
votes
2
replies
201
views
edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
6 weeks ago Marianna ▴ 20
0
votes
2
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219
views
Clarification on Library Size Normalization After Using tximport with countsFromAbundance="lengthScaledTPM"
tximport
updated 8 weeks ago by 42k • written 8 weeks ago by • 0
2
votes
1
reply
274
views
Creating data matrix in Deseq2 from tximport data invalid class SummarizedExperiment object
DESeq2 tximport
updated 10 weeks ago by ★ 4.1k • written 10 weeks ago by • 0
2
votes
3
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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 5 months ago by ★ 1.4k • written 5 months ago by • 0
0
votes
1
reply
371
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
590
views
tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
tximport DESeq2
updated 5 months ago by 66k • written 5 months ago by • 0
0
votes
3
replies
454
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
10
votes
11
replies
2.0k
views
tximport error: vroom
tximport
updated 6 months ago by • 0 • written 7 months ago by ▴ 40
2
votes
3
replies
846
views
Import Salmon data with tximport and pool technical replicates
tximport edgeR
written 9 months ago by • 0
4
votes
13
replies
1.5k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport DESeq2
updated 7 months ago by 42k • written 8 months ago by • 0
0
votes
4
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930
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
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
0
votes
2
replies
688
views
tximport error in reading salmon output files?
tximport tximportData
updated 3 months ago by • 0 • written 11 months ago by • 0
0
votes
1
reply
647
views
Which file in tximport should I use for DESeq2 analysis?
tximport DESeq2
updated 12 months ago by 66k • 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
855
views
Error in H5Fopen
rhdf5 Rhdf5lib kallisto tximport
13 months ago • updated 12 months ago Yijing • 0
1
vote
3
replies
893
views
tximport error
tximport r
updated 13 months ago by 42k • written 13 months ago by • 0
0
votes
2
replies
949
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
6
votes
10
replies
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
1
reply
755
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
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2
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832
views
how to match salmon output to txname
GenomicFeatures tximport salmon
written 16 months ago by • 0
0
votes
1
reply
771
views
Missing transcript
DESeq2 tximport salmon
updated 16 months ago by ★ 4.1k • written 16 months ago by • 0
2
votes
1
reply
712
views
Confused about tximport-DESeq2 setup
DESeq2 tximport salmon
updated 16 months ago by ★ 4.1k • written 16 months 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
804
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 66k • written 18 months ago by ▴ 10
0
votes
1
reply
916
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
813
views
error loading kallisto output in tximport
file.exists false kallisto tximport
18 months ago cta • 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
3
votes
3
replies
965
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
1
vote
2
replies
1.6k
views
transcripts missing from tx2gene
tximport
20 months ago Erick • 0
0
votes
1
reply
650
views
tximport: not all(file.exists(files)) are true
tximport
updated 20 months ago by 42k • 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
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
0
votes
3
replies
995
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
0
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4
replies
1.1k
views
Alternative for wininet method in tximeta
DESeq2 tximport tximportData tximeta
23 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
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
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
0
votes
1
reply
863
views
Why TxImport Abundance is slightly different from manually added TPMs?
tximport R
updated 2.0 years ago by 42k • written 2.0 years ago by • 0
2
votes
3
replies
1.2k
views
Problem with tximport IDs
tximport tx2gene rnas DESeq2 RNASeqData
2.1 years ago Maka • 0
6
votes
4
replies
2.4k
views
confused with tximport counts abundance using salmon input
RNASeq tximport
2.1 years ago Al90 ▴ 10
0
votes
2
replies
2.5k
views
tximport ERROR : all(file.exists(files)) is not TRUE
Linux R tximport
2.2 years ago nakane_clan • 0
2
votes
5
replies
1.8k
views
from kallisto to deseq2 analysis
biomaRt DESeq2 tximport
2.3 years ago Marianna ▴ 20
2
votes
3
replies
975
views
Import RSEM output without sample data
DESeq2 tximportData tximport
updated 2.3 years ago by 42k • written 2.3 years ago by • 0
50 results • Page 1 of 1
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Answer: Documenting resources in an `ExperimentHub` package? by James W. MacDonald 66k
The easiest way to do that IMO is to use emacs/ESS (or I believe there is some newfangled thing called RStudio? Not personally familiar, bu…
Comment: ChAMP installation issue by shepherl 3.9k
We are still waiting for the goseq to respond to our requests but will take action next week if it is not resolved. ChAMP is currently una…
Comment: How to arrange multiple plots into one page in NOISeq? by baptiste.bidon • 0
After facing the same problem, I realise that you can direct your plot in the matrix with the *par()* option `par(..., mfg = c(1,2))`. If i…
Comment: ChAMP installation issue by Tahirah • 0
Hello. Could you please share how you managed to install ChAMP in R 4.4.0? I also have R 4.4.0 and Bioconductor 3.19 version and ChAMP fail…
Answer: Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data by James W. MacDonald 66k
Yes, you can use `limma`.
Votes
how to control age and gender effect in expression data using DESeq2
Answer: Error retrieving ensembl gene id using biomaRt...
Comment: LRT, more than two conditions and pairwise comparisons
Answer: Control group between 2 batches have different expression in RNAseq data
Answer: How to remove batch effect to combine RNAseq data from 2 different experiments?
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