Showing : tximport • reset
32
votes
16
replies
16k
views
difference among tximport scaledTPM, lengthScaledTPM and the original TPM output by salmon/kallisto
tximport deseq2 TPM RPKM rnaseq
updated 5.4 years ago by ▴ 20 • written 7.2 years ago by ▴ 190
14
votes
25
replies
2.2k
views
dtuScaledTPM vs lengthScaledTPM in DTU analysis
tximport dtu salmon TPM rnaseqDTU
written 4.5 years ago by ▴ 60
9
votes
2
replies
7.7k
views
Using RSEM with tximport and DESeq2
deseq2 tximport software error bug
updated 2.0 years ago by 40k • written 6.6 years ago by ▴ 10
9
votes
4
replies
3.0k
views
GC/length bias correction in gene expression quantification - Is CQN necessary if using Salmon --GCBias option?
salmon cqn tximport deseq2 rnaseq
updated 6.6 years ago by 40k • written 6.6 years ago by ▴ 30
9
votes
11
replies
5.2k
views
Using 'tximport' library for downstream DGE after quantifying with Kallisto
tximport Kallisto rna-seq
updated 6.6 years ago by ▴ 20 • written 7.4 years ago by ▴ 10
8
votes
12
replies
3.3k
views
How to create tx2gene data.frame when there's no TxDb object for the organism you are working with.
tximport deseq2 annotationdbi
updated 6.0 years ago by ★ 2.0k • written 6.0 years ago by • 0
7
votes
17
replies
4.9k
views
DESeqDataSetFromTximport: Error in checkSlotAssignment
deseq2 tximport
6.4 years ago JWCarlson ▴ 80
7
votes
8
replies
3.2k
views
R failing to load genome files from EnsDb.Hsapiens.v86
tximport ensembldb EnsDB.hsapiens.v86
updated 4.7 years ago by 0 • written 4.8 years ago by ▴ 20
6
votes
2
replies
929
views
tximport + edgeR not recommended?
tximport edgeR
updated 3.2 years ago by 40k • written 3.2 years ago by • 0
6
votes
6
replies
1.9k
views
Transformation of raw RSEM gene expression estimates with variance stabilizing transformation and tximport R package
DESeq2 VST rsem tximport
2.8 years ago svlachavas ▴ 810
6
votes
4
replies
4.3k
views
Is there any point to TMM-normalize TPM prior to limma-voom?
voom limma-voom tximport edger
updated 6.5 years ago by 7.8k • written 6.5 years ago by ▴ 10
5
votes
4
replies
1.5k
views
confused with tximport counts abundance using salmon input
RNASeq tximport
17 months ago Al90 ▴ 10
5
votes
10
replies
9.4k
views
Constructing tx2gene for Salmon txImport Quantification using Gencode Mouse Transcript Annotation
Michael Love Salmon tximport tx2gene
updated 5.6 years ago by 40k • written 5.6 years ago by ▴ 30
5
votes
9
replies
4.7k
views
Trouble with Tximport
tximport salmon
updated 7.4 years ago by 40k • written 7.4 years ago by ▴ 30
5
votes
9
replies
3.1k
views
Correct version of EnsDb.Hsapiens for ensembl transcriptome
ensembldb ensembl release rnaseq salmon tximport
5.6 years ago emmak ▴ 20
5
votes
5
replies
4.2k
views
tximport transcript missing
deseq2 salmon tximport
4.2 years ago mr6518849 ▴ 10
5
votes
5
replies
2.5k
views
Problem with tximport(reader = read_tsv) and workaround
tximport readr read_tsv
updated 7.0 years ago by 40k • written 7.0 years ago by ★ 2.0k
5
votes
11
replies
1.6k
views
Correct use of tximport in combination with edgeR cpm()
tximport edgeR
4.4 years ago • updated 3.7 years ago ATpoint ★ 3.4k
5
votes
3
replies
2.7k
views
Full length single-cell RNA-seq - tximport output for downstream analysis
tximport Seurat Smart-Seq Smart-Seq2
updated 3.2 years ago by 40k • written 3.2 years ago by ▴ 40
5
votes
6
replies
929
views
Selecting individual samples from tximport and DGE matrix design with missing biological replicate
DESeq2 limma tximport
updated 12 months ago by 48k • written 12 months ago by • 0
5
votes
6
replies
2.6k
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 3.9 years ago by ★ 3.0k • written 4.0 years ago by ▴ 80
4
votes
3
replies
4.0k
views
txtimportData installation on R version 3.3.0 (2016-05-03)
tximport deseq2
7.2 years ago jarod_v6@libero.it ▴ 40
4
votes
5
replies
1.4k
views
GAGE after tximport
gage tximport
updated 5.9 years ago by ★ 1.6k • written 5.9 years ago by ▴ 230
4
votes
9
replies
1.9k
views
tximport recommendation for limma-trend downstream analysis?
tximport limma limma-trend edgeR
updated 6.0 years ago by ★ 28k • written 6.0 years ago by ★ 2.0k
4
votes
14
replies
2.5k
views
running tximport for salmon quants
tximport readr
updated 7.3 years ago by 40k • written 7.3 years ago by • 0
4
votes
7
replies
3.1k
views
Analyzing TCGA RSEM Data with DESeq2 downloaded from FireBrowse
deseq2 tximport tcga rsem firebrowse
updated 3.3 years ago by 3.8k • written 3.3 years ago by • 0
4
votes
1
reply
922
views
Correlation of gene expression values using tpms and normalized counts
tximport deseq2
updated 4.4 years ago by 40k • written 4.4 years ago by ▴ 20
4
votes
3
replies
3.0k
views
tximport error: all(names(aveLengthSampGene) == rownames(lengthMat)) is not TRUE
tximport salmon R bioconductor
updated 21 months ago by • 0 • written 6.2 years ago by • 0
4
votes
9
replies
3.8k
views
How to get DESeq2 sizefactors from data imported using tximport
deseq2 sailfish tximport
updated 4 months ago by • 0 • written 6.2 years ago by • 0
4
votes
3
replies
603
views
tx2gene object trouble when working with kallisto and A.thaliana
tx2gene tximport Arabidopsis_thaliana kallisto
updated 10 months ago by 63k • written 10 months ago by ▴ 10
4
votes
3
replies
1.0k
views
Concatenating expression counts from different RNA-seq quantification tools
tximport HERVs edgeR DESeq2
updated 2.3 years ago by 40k • written 2.3 years ago by ▴ 30
4
votes
3
replies
860
views
Trouble with Tximport for edgeR
tximport edger
updated 5.6 years ago by 48k • written 5.6 years ago by • 0
4
votes
3
replies
1.2k
views
Cannot extract size factor from DESeq2 analysis
deseq2 tximport
3.4 years ago zroger499 • 0
4
votes
3
replies
1.4k
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
5.5 years ago pvd2107 ▴ 30
3
votes
2
replies
1.4k
views
tximport with versioned identifiers
tximport ensembldb
5.9 years ago Ed Siefker ▴ 230
3
votes
1
reply
804
views
tximport rowsum error
tximport
2.6 years ago Ezgi ▴ 60
3
votes
5
replies
2.4k
views
txImport: a gene seems missing from the sample data
txImportData txImport
updated 2.7 years ago by 63k • written 6.6 years ago by • 0
3
votes
1
reply
2.5k
views
Gene level exploratory data analysis from tximport results
tximport edgeR DESeq2
updated 7.3 years ago by 40k • written 7.3 years ago by 13k
3
votes
5
replies
1.5k
views
edgeR + tximport: calcNormFactors and the usage of offsets
edgeR tximport differential expression
3.4 years ago • updated 3.3 years ago hollandademello • 0
3
votes
3
replies
1.2k
views
Kallisto with tximport gives different results with asymmetrical experimental design
kallisto deseq2 tximport
updated 6.0 years ago by 40k • written 6.0 years ago by ▴ 20
3
votes
11
replies
2.3k
views
should I use rsem's summary to genes or tximport's?
tximport
updated 7.3 years ago by 40k • written 7.3 years ago by ▴ 10
3
votes
2
replies
6.0k
views
Non-integer counts from tximport OK for edgeR / DESeq2?
tximport edgeR DESeq2
updated 6.9 years ago by 40k • written 6.9 years ago by ★ 2.0k
3
votes
5
replies
2.2k
views
DESeqDataSetFromTximport with kallisto abundances.
deseq2 tximport
updated 6.0 years ago by • 0 • written 6.3 years ago by ▴ 30
3
votes
4
replies
3.0k
views
Importing RSEM transcript-level data using tximport
tximport rsem
updated 5.8 years ago by 40k • written 5.8 years ago by ▴ 10
3
votes
13
replies
1.9k
views
tximport's parameter for countsFromAbundance doesn't work
tximport rsem edger
5.6 years ago tim.ivanov.92 • 0
3
votes
1
reply
423
views
Can tximport be used to mitigate sample specific length biases?
RNASeq tximport
updated 3.8 years ago by 40k • written 3.8 years ago by ▴ 30
3
votes
4
replies
1.3k
views
quant.sf files and tximport, transcripts not recognized
salmon tximport
updated 4.5 years ago by 40k • written 4.5 years ago by ▴ 10
3
votes
2
replies
973
views
Correct usage of tximport counts in edgeR without offset matrix.
tximport edgeR rna-seq
updated 4.8 years ago by 63k • written 4.8 years ago by • 0
3
votes
9
replies
4.1k
views
txi <- tximport(files, type="salmon", tx2gene=tx2gene) Error in tximport(files, type = "salmon", tx2gene = tx2gene) : all(file.exists(files)) is n…
deseq2 tximport file.path files file.exists
4.6 years ago • updated 4.5 years ago Leo K • 0
3
votes
4
replies
1.2k
views
tximport and de novo transcriptome
tximport salmon rna seq de novo
updated 5.0 years ago by 63k • written 5.0 years ago by ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Answer: DelayedArray::read_sparse_block by Hervé Pagès 16k
Hi Koki, Sorry again for the slow response. `read_sparse_block()` has been around for years. It's a generic function defined in the *…
Comment: Speeding up of DelayedArray::write_block() by Hervé Pagès 16k
Sorry for missing that one too. When writting blocks to an HDF5 file, the `write_block()` method for HDF5RealizationSink or TENxRealizatio…
Comment: Speeding up of DelayedArray::write_block() by Hervé Pagès 16k
Hi Koki, sorry for not seeing this before. > will SparseArraySeed in DelayedArray be replaced by this new sparse array format? Yes it wil…
Comment: Manual creation of qPCRset does not work by Ed Siefker ▴ 230
Thanks! This works for me.
Answer: Manual creation of qPCRset does not work by James W. MacDonald 63k
``` > mat <- matrix(rnorm(6*96), ncol = 6, nrow = 96, byrow = FALSE) > pd <- new("AnnotatedDataFrame", data = data.frame(1:6, row.names …
Votes
Comment: List of Deprecated Packages for Bioc3.18
Answer: Manual creation of qPCRset does not work
Answer: MDS plot edgeR
A: legend with gradient in ComplexHeatmap
Comment: comparing contrasts in edger/lima using makeContrasts function
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