Showing : tximport • reset
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
2
votes
19
replies
2.1k
views
tximport returns NA counts
tximport
5.8 years ago leonfodoulian • 0
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
7
votes
17
replies
4.9k
views
DESeqDataSetFromTximport: Error in checkSlotAssignment
deseq2 tximport
6.4 years ago JWCarlson ▴ 80
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
2
votes
14
replies
1.5k
views
Salmon (quant.sf) to tximport error
tximport
updated 4.5 years ago by 40k • written 4.5 years ago by ▴ 10
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
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
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
11
replies
1.4k
views
failure importing data with tximport with error information
software error tximport hdf5
updated 3.9 years ago by 40k • written 3.9 years ago by ▴ 10
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
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
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
1
vote
11
replies
6.5k
views
RNA Seq data analysis using Salmon and tximport
RNAseq tximport
6.0 years ago tanyabioinfo ▴ 20
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
10
replies
1.8k
views
tximport Error in attr(x, "names") <- as.character(value) : 'names' attribute [2] must be the same length as the vector [1]
software error RNAseq tximport R
updated 4.1 years ago by 40k • written 4.1 years ago by • 0
1
vote
9
replies
1.1k
views
Question: Error running summarizeToGene() - RNA Seq Bioconductor pipeline
tximeta tximport deseq2
updated 3.0 years ago by 40k • written 3.0 years ago by ▴ 20
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
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
2
votes
9
replies
1.1k
views
Tximport of quasi-alignment-based RNAseq quantification (Salmon) for use with edgeR
salmon edger tximport rnaseq
updated 5.3 years ago by ★ 28k • written 5.3 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
2
votes
9
replies
595
views
Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport tximportData DESeq2
11 weeks ago • updated 10 weeks ago Ndimensional ▴ 20
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
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
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
1
vote
9
replies
2.0k
views
error in aSwitchlist (isoformswitchanalyzeR)
isoformswitchanalyzeR tximport rnaseq salmon
updated 4.5 years ago by ▴ 120 • written 4.5 years ago by • 0
2
votes
9
replies
1.6k
views
Unused argument of reader = read_tsv on R version 3.4.1
tximport
6.1 years ago tarun2 • 0
2
votes
8
replies
1.1k
views
RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM tximport scRNAseq DESeq2
15 months ago • updated 14 months ago Kelen ▴ 10
0
votes
8
replies
1.5k
views
tximport not working on tsv files
tximport
4.1 years ago HKS • 0
0
votes
8
replies
1.1k
views
tximport question on the values contained in "counts" and "abundance" matrices
tximport
updated 4.6 years ago by 63k • written 4.6 years ago by • 0
2
votes
8
replies
553
views
Silent error in tximport after installing GEOquery
tximport
4.0 years ago penny.lane • 0
0
votes
8
replies
1.3k
views
Importing RSEM with tximport
tximport RSEM import error
updated 3.1 years ago by 40k • written 3.1 years ago by ▴ 60
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
1
vote
8
replies
2.4k
views
IgnoreTxVersion on Tximport not working
Tximport Salmon
4.0 years ago k1m ▴ 20
0
votes
8
replies
2.2k
views
Differences in gene length passed to DESeq2 by tximport reulted in different gene rankings
deseq2 tximport rsem saimon
updated 5.3 years ago by 40k • written 5.3 years ago by • 0
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
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
7
replies
1.5k
views
RNA-seq with Salmon and tximport
RNA-seq Salmon tximport
updated 4.1 years ago by 63k • written 4.1 years ago by • 0
2
votes
7
replies
1.5k
views
Obtaining transcript names in RSEM
tximport rsem
updated 6.0 years ago by 40k • written 6.0 years ago by ▴ 20
3
votes
7
replies
551
views
failed to use tximport for creating count matrix from kallisto
tximport kallisto
4 months ago Yijing • 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 3.4 years ago by • 0
1
vote
7
replies
1.6k
views
tximport from RSEM expected counts: is it possible to import from a table rather than a file?
tximport limma rnaseq
updated 2.5 years ago by • 0 • written 3.4 years ago by ▴ 50
2
votes
7
replies
1.7k
views
Get the countsFromAbundance as limma input
tximport limma deseq2 differential expression
updated 5.1 years ago by 48k • written 5.1 years ago by • 0
1
vote
7
replies
1.6k
views
How to merge two tximport object into one dataset for DESeqDataSetFromTximport
deseq2 tximport
updated 4.2 years ago by 40k • written 4.2 years ago by • 0
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
0
votes
7
replies
808
views
tximeta doesn't work downloading the ref genome
deseq2 tximeta tximport rnaseq
3.6 years ago rafaelsolersanblas ▴ 50
0
votes
7
replies
1.4k
views
Problem with Tximport
tximportData tximport
2.6 years ago agoesmartini • 0
0
votes
6
replies
1.7k
views
[deseq2] normalization between samples after merging transcripts into genes
deseq2 tximport
updated 4.6 years ago by 40k • written 4.6 years ago by • 0
2
votes
6
replies
1.9k
views
How to run tximport ?
tximport
updated 3.2 years ago by ★ 3.4k • written 3.2 years ago by • 0
2
votes
6
replies
1.3k
views
[DESeq2] Different results from tutorial
deseq2 tximportdata tximport
updated 5.3 years ago by 40k • written 5.3 years ago by • 0
50 results • Page 1 of 1
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Comment: List of Deprecated Packages for Bioc3.18 by Hervé Pagès 16k
Also the source package is not available [in BioC 3.17](https://bioconductor.org/packages/3.17/CancerInSilico) which means that the package…
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.
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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