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
0
votes
1
reply
11k
views
there is no "tx2gene.gencode.v27.csv" in tximportData
tximport
updated 5.4 years ago by 40k • written 5.4 years ago by • 0
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
0
votes
4
replies
8.2k
views
tximport all(file.exists(files)) is not TRUE
bioconductor tximport rnaseq R
7.0 years ago ctl • 0
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
1
vote
11
replies
6.5k
views
RNA Seq data analysis using Salmon and tximport
RNAseq tximport
6.0 years ago tanyabioinfo ▴ 20
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
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
7
votes
17
replies
4.9k
views
DESeqDataSetFromTximport: Error in checkSlotAssignment
deseq2 tximport
6.4 years ago JWCarlson ▴ 80
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
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
5
replies
4.2k
views
tximport transcript missing
deseq2 salmon tximport
4.2 years ago mr6518849 ▴ 10
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
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
1
vote
3
replies
3.9k
views
PCA from TPM
pca tpm tximport
5.9 years ago tanyabioinfo ▴ 20
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
0
votes
3
replies
3.8k
views
Create Ensembl transcript to gene IDs table with R ensembldb package for tximport
ensembldb tximport salmon
updated 5.3 years ago by ★ 2.0k • written 5.3 years ago by ▴ 30
1
vote
2
replies
3.8k
views
Importing data into the DESeq2 pipeline using tximport
DESeq2 tximport
2.6 years ago Nikolay Ivanov • 0
2
votes
4
replies
3.7k
views
tximport, Kallisto and Deseq2 (quick answer)
kallisto tximport deseq2 counts
4.4 years ago • updated 3.5 years ago Mozart ▴ 20
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
2
votes
5
replies
3.2k
views
unable to get tximport to work on data from kallisto
tximport kallisto
updated 6.4 years ago by 13k • written 6.4 years ago by ▴ 10
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
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
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
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
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
2
votes
8
replies
3.0k
views
Which R version is needed for tximport package?
tximport package R version install tximport
3.1 years ago harelarik ▴ 60
2
votes
18
replies
3.0k
views
Using tximport on rsem files produces error while trying to read in files
R tximport rnaseq tpm rsem
5.5 years ago stephan.emmrich ▴ 10
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
0
votes
4
replies
2.8k
views
Tutorial: Importing multiple .h5 files using tximport
tximport Tutorial
updated 5.4 years ago by 13k • written 5.4 years ago by ▴ 10
1
vote
5
replies
2.8k
views
tximport using for data generated from other tools
tximport salmon eXpress
updated 5.4 years ago by 40k • written 6.3 years ago by • 0
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
0
votes
6
replies
2.6k
views
Salmon, tximport and DeSeq2 for differential expression analysis of 3' biased data
tximport DESeq2 "tximport" deseq2 salmon
6.3 years ago sunil.mangalam • 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 3.9 years ago by ▴ 80
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
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
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
1
vote
5
replies
2.4k
views
tximport error with kallisto .h5 files
deseq2 kallisto tximport
updated 4.7 years ago by 40k • written 4.7 years ago by • 0
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
2
votes
6
replies
2.4k
views
Subsetting a tximport object
tximport
written 5.5 years ago by • 0
1
vote
9
replies
2.4k
views
Importing Kallisto counts with tximport
tximport Kallisto H5Fopen
updated 3.4 years ago by 40k • written 3.4 years ago by • 0
1
vote
8
replies
2.4k
views
IgnoreTxVersion on Tximport not working
Tximport Salmon
4.0 years ago k1m ▴ 20
2
votes
7
replies
2.3k
views
tximport - using hg38 with RefSeq (NM) and Gene Symbol
salmon hg38 tximport tx2gene.csv
updated 6.5 years ago by 40k • written 6.5 years ago by • 0
2
votes
3
replies
2.3k
views
Getting between sample/within sample normalized gene expression values from DESeq2
rnaseq deseq2 tximport salmon normalization
updated 6.3 years ago by 40k • written 6.3 years ago by • 0
1
vote
5
replies
2.3k
views
RNA-seq analysis on mouse data with human contamination in controls
rna-seq salmon tximport limma
updated 6.4 years ago by ★ 28k • written 6.4 years ago by ▴ 70
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
1
vote
4
replies
2.2k
views
If transcript-to-gene conversion is needed in kallisto > tximport > DESeq2 pipeline
deseq2 rnaseq kallisto tximport
updated 5.5 years ago by 40k • written 5.5 years ago by • 0
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
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
0
votes
7
replies
2.2k
views
Error reading kallisto files using tximport for cross species RNA-Seq analysis
kallisto tximport RNA-Seq across species
updated 22 months ago by • 0 • written 6.3 years ago by ▴ 40
50 results • Page 1 of 1
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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
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
Answer: comparing contrasts in edger/lima using makeContrasts function
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