Showing : Tximport • reset
32
votes
16
replies
19k
views
difference among tximport scaledTPM, lengthScaledTPM and the original TPM output by salmon/kallisto
tximport deseq2 TPM RPKM rnaseq
updated 6.8 years ago by ▴ 20 • written 8.5 years ago by ▴ 200
16
votes
25
replies
3.8k
views
dtuScaledTPM vs lengthScaledTPM in DTU analysis
tximport dtu salmon TPM rnaseqDTU
written 5.8 years ago by ▴ 60
10
votes
11
replies
2.9k
views
tximport error: vroom
tximport
updated 15 months ago by • 0 • written 15 months ago by ▴ 40
9
votes
11
replies
5.9k
views
Using 'tximport' library for downstream DGE after quantifying with Kallisto
tximport Kallisto rna-seq
updated 7.9 years ago by ▴ 20 • written 8.8 years ago by ▴ 10
9
votes
4
replies
3.9k
views
GC/length bias correction in gene expression quantification - Is CQN necessary if using Salmon --GCBias option?
salmon cqn tximport deseq2 rnaseq
updated 7.9 years ago by 43k • written 7.9 years ago by ▴ 30
9
votes
2
replies
9.9k
views
Using RSEM with tximport and DESeq2
deseq2 tximport software error bug
updated 3.4 years ago by 43k • written 7.9 years ago by ▴ 10
8
votes
12
replies
4.4k
views
How to create tx2gene data.frame when there's no TxDb object for the organism you are working with.
tximport deseq2 annotationdbi
updated 7.3 years ago by ★ 2.1k • written 7.3 years ago by • 0
7
votes
17
replies
6.1k
views
DESeqDataSetFromTximport: Error in checkSlotAssignment
deseq2 tximport
7.7 years ago JWCarlson ▴ 80
7
votes
8
replies
4.5k
views
R failing to load genome files from EnsDb.Hsapiens.v86
tximport ensembldb EnsDB.hsapiens.v86
updated 6.0 years ago by 0 • written 6.2 years ago by ▴ 20
6
votes
7
replies
3.2k
views
edgeR + tximport: calcNormFactors and the usage of offsets
edgeR tximport differential expression
updated 24 days ago by 52k • written 4.7 years ago by ▴ 20
6
votes
3
replies
3.6k
views
Full length single-cell RNA-seq - tximport output for downstream analysis
tximport Seurat Smart-Seq Smart-Seq2
updated 4.5 years ago by 43k • written 4.5 years ago by ▴ 40
6
votes
6
replies
2.7k
views
Transformation of raw RSEM gene expression estimates with variance stabilizing transformation and tximport R package
DESeq2 VST rsem tximport
4.2 years ago svlachavas ▴ 840
6
votes
11
replies
2.6k
views
Correct use of tximport in combination with edgeR cpm()
tximport edgeR
5.7 years ago • updated 5.0 years ago ATpoint ★ 4.6k
6
votes
10
replies
2.8k
views
Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
updated 9 months ago by • 0 • written 23 months ago by ▴ 10
6
votes
4
replies
3.5k
views
confused with tximport counts abundance using salmon input
RNASeq tximport
2.8 years ago Al90 ▴ 10
6
votes
4
replies
5.3k
views
Is there any point to TMM-normalize TPM prior to limma-voom?
voom limma-voom tximport edger
updated 7.8 years ago by ★ 7.9k • written 7.8 years ago by ▴ 10
6
votes
2
replies
1.3k
views
tximport + edgeR not recommended?
tximport edgeR
updated 4.6 years ago by 43k • written 4.6 years ago by • 0
5
votes
5
replies
5.6k
views
tximport transcript missing
deseq2 salmon tximport
5.5 years ago mr6518849 ▴ 10
5
votes
9
replies
3.9k
views
Correct version of EnsDb.Hsapiens for ensembl transcriptome
ensembldb ensembl release rnaseq salmon tximport
7.0 years ago emmak ▴ 20
5
votes
6
replies
4.2k
views
How to build and map to a "pre-mRNA" reference transcriptome for single nucleus RNA-seq data?
tximeta ensembldb single-cell snRNA-seq tximport
updated 5.3 years ago by ★ 3.4k • written 5.3 years ago by ▴ 80
5
votes
5
replies
3.3k
views
Problem with tximport(reader = read_tsv) and workaround
tximport readr read_tsv
updated 8.3 years ago by 43k • written 8.3 years ago by ★ 2.0k
5
votes
6
replies
2.0k
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 2.4 years ago by • 0
5
votes
2
replies
1.8k
views
Correct usage of tximport counts in edgeR without offset matrix.
tximport edgeR rna-seq
updated 6.2 years ago by 67k • written 6.2 years ago by • 0
5
votes
9
replies
6.0k
views
Trouble with Tximport
tximport salmon
updated 8.8 years ago by 43k • written 8.8 years ago by ▴ 30
5
votes
10
replies
13k
views
Constructing tx2gene for Salmon txImport Quantification using Gencode Mouse Transcript Annotation
Michael Love Salmon tximport tx2gene
updated 6.9 years ago by 43k • written 6.9 years ago by ▴ 30
4
votes
3
replies
4.4k
views
txtimportData installation on R version 3.3.0 (2016-05-03)
tximport deseq2
8.6 years ago jarod_v6@libero.it ▴ 40
4
votes
6
replies
2.6k
views
Using spike-in RNA for normalization of Salmon counts imported using Tximport
deseq2 Tximport Sizefactors normalizationfactors spike-in
updated 4.6 years ago by 43k • written 4.6 years ago by • 0
4
votes
9
replies
2.7k
views
tximport recommendation for limma-trend downstream analysis?
tximport limma limma-trend edgeR
updated 7.3 years ago by ★ 28k • written 7.3 years ago by ★ 2.0k
4
votes
14
replies
3.2k
views
running tximport for salmon quants
tximport readr
updated 8.6 years ago by 43k • written 8.6 years ago by • 0
4
votes
7
replies
4.9k
views
Analyzing TCGA RSEM Data with DESeq2 downloaded from FireBrowse
deseq2 tximport tcga rsem firebrowse
updated 4.7 years ago by ★ 4.0k • written 4.7 years ago by • 0
4
votes
3
replies
3.8k
views
tximport error: all(names(aveLengthSampGene) == rownames(lengthMat)) is not TRUE
tximport salmon R bioconductor
updated 3.1 years ago by • 0 • written 7.5 years ago by • 0
4
votes
3
replies
1.7k
views
Concatenating expression counts from different RNA-seq quantification tools
tximport HERVs edgeR DESeq2
updated 3.7 years ago by 43k • written 3.7 years ago by ▴ 40
4
votes
9
replies
5.0k
views
How to get DESeq2 sizefactors from data imported using tximport
deseq2 sailfish tximport
updated 20 months ago by • 0 • written 7.6 years ago by • 0
4
votes
5
replies
696
views
DESeq Input from Salmon + tximport/tximeta
tximportData summarizeToGene tximport DESeq2 salmon
11 weeks ago LuciaNhu • 0
4
votes
1
reply
1.3k
views
Correlation of gene expression values using tpms and normalized counts
tximport deseq2
updated 5.7 years ago by 43k • written 5.7 years ago by ▴ 20
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 67k • written 2.2 years ago by ▴ 10
4
votes
3
replies
1.9k
views
Selecting Correct Set of Gene IDs from Mouse Gencode GFF3 for RNA Seq Analysis (Removing Genes without symbols)
deseq2 tximport org.mm.eg.db gencode
6.8 years ago pvd2107 ▴ 30
4
votes
5
replies
2.0k
views
GAGE after tximport
gage tximport
updated 7.2 years ago by ★ 1.6k • written 7.2 years ago by ▴ 230
4
votes
13
replies
2.8k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport DESeq2
updated 16 months ago by 43k • written 17 months ago by • 0
4
votes
3
replies
1.2k
views
Trouble with Tximport for edgeR
tximport edger
updated 7.0 years ago by 52k • written 7.0 years ago by • 0
4
votes
3
replies
2.2k
views
Cannot extract size factor from DESeq2 analysis
deseq2 tximport
4.7 years ago zroger499 • 0
3
votes
2
replies
1.8k
views
tximport with versioned identifiers
tximport ensembldb
7.3 years ago Ed Siefker ▴ 230
3
votes
5
replies
3.0k
views
txImport: a gene seems missing from the sample data
txImportData txImport
updated 4.0 years ago by 67k • written 7.9 years ago by • 0
3
votes
1
reply
1.3k
views
tximport rowsum error
tximport
3.9 years ago Ezgi ▴ 60
3
votes
1
reply
2.9k
views
Gene level exploratory data analysis from tximport results
tximport edgeR DESeq2
updated 8.6 years ago by 43k • written 8.6 years ago by ★ 13k
3
votes
3
replies
1.6k
views
Kallisto with tximport gives different results with asymmetrical experimental design
kallisto deseq2 tximport
updated 7.3 years ago by 43k • written 7.3 years ago by ▴ 20
3
votes
11
replies
2.9k
views
should I use rsem's summary to genes or tximport's?
tximport
updated 8.7 years ago by 43k • written 8.7 years ago by ▴ 10
3
votes
2
replies
7.3k
views
Non-integer counts from tximport OK for edgeR / DESeq2?
tximport edgeR DESeq2
updated 8.3 years ago by 43k • written 8.3 years ago by ★ 2.0k
3
votes
5
replies
2.6k
views
DESeqDataSetFromTximport with kallisto abundances.
deseq2 tximport
updated 7.3 years ago by • 0 • written 7.6 years ago by ▴ 30
3
votes
4
replies
4.3k
views
Importing RSEM transcript-level data using tximport
tximport rsem
updated 7.2 years ago by 43k • written 7.2 years ago by ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Answer: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Following the discussion of this post, the package [gDNAx](https://bioconductor.org/packages/gDNAx) has been fixed in devel and release 1.4…
Answer: Selection of correct coefficients or contrasts in DESeq2 by James W. MacDonald 67k
Using R's model formulation for three-way interactions is probably not the way to go here. Or at least I wouldn't do it that way. An easier…
Comment: How to generate circular cnetplot and color nodes and edges in the same plot ? by Blandine • 0
Thank you so much ! It's working !
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by James W. MacDonald 67k
Yes. If you have the Illumina IDs, then all the annotation data that `cpg.annotate` uses will be based on hg19. It doesn't matter if TCGA l…
Comment: Recount3 data correspond to TCGA data by Leonardo Collado Torres ★ 1.1k
Thanks @fep29! ^^
Votes
Comment: Recount3 data correspond to TCGA data
Answer: DESeq2- merging technical vs biological replicates
Answer: SingleCellExperiment convenience function for metadata+expression?
How to correct for tumor purity using DESeq2 to analyze TCGA tumor sample expression.
Answer: EdgeR Biological CVs
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