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
0
votes
1
reply
14k
views
there is no "tx2gene.gencode.v27.csv" in tximportData
tximport
updated 6.7 years ago by 43k • written 6.7 years ago by • 0
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
0
votes
5
replies
10k
views
tximport all(file.exists(files)) is not TRUE
bioconductor tximport rnaseq R
updated 10 months ago by • 0 • written 8.3 years ago by • 0
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
1
vote
11
replies
7.8k
views
RNA Seq data analysis using Salmon and tximport
RNAseq tximport
7.3 years ago tanyabioinfo ▴ 20
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
7
votes
17
replies
6.1k
views
DESeqDataSetFromTximport: Error in checkSlotAssignment
deseq2 tximport
7.7 years ago JWCarlson ▴ 80
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
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
3
votes
9
replies
5.7k
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
5.9 years ago Leo K • 0
5
votes
5
replies
5.6k
views
tximport transcript missing
deseq2 salmon tximport
5.5 years ago mr6518849 ▴ 10
2
votes
4
replies
5.6k
views
tximport, Kallisto and Deseq2 (quick answer)
kallisto tximport deseq2 counts
5.8 years ago • updated 4.8 years ago Mozart ▴ 30
2
votes
2
replies
5.4k
views
Importing data into the DESeq2 pipeline using tximport
DESeq2 tximport
3.9 years ago Nikolay Ivanov • 0
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
1
vote
3
replies
5.1k
views
PCA from TPM
pca tpm tximport
7.3 years ago tanyabioinfo ▴ 20
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
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
0
votes
3
replies
4.8k
views
Create Ensembl transcript to gene IDs table with R ensembldb package for tximport
ensembldb tximport salmon
updated 6.7 years ago by ★ 2.1k • written 6.7 years ago by ▴ 30
2
votes
8
replies
4.5k
views
Which R version is needed for tximport package?
tximport package R version install tximport
4.4 years ago harelarik ▴ 60
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
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
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
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
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
2
votes
5
replies
4.0k
views
unable to get tximport to work on data from kallisto
tximport kallisto
updated 7.7 years ago by ★ 13k • written 7.7 years ago by ▴ 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
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
2
votes
18
replies
3.9k
views
Using tximport on rsem files produces error while trying to read in files
R tximport rnaseq tpm rsem
6.8 years ago stephan.emmrich ▴ 10
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
0
votes
4
replies
3.8k
views
Tutorial: Importing multiple .h5 files using tximport
tximport Tutorial
updated 6.7 years ago by ★ 13k • written 6.7 years ago by ▴ 10
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
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
2
votes
6
replies
3.6k
views
Subsetting a tximport object
tximport
written 6.9 years ago by • 0
1
vote
5
replies
3.6k
views
tximport using for data generated from other tools
tximport salmon eXpress
updated 6.7 years ago by 43k • written 7.7 years ago by • 0
1
vote
5
replies
3.5k
views
tximport error: all(txId == raw[[txIdCol]]) is not TRUE
tximport
updated 18 months ago by 43k • written 3.2 years ago by • 0
1
vote
9
replies
3.5k
views
Importing Kallisto counts with tximport
tximport Kallisto H5Fopen
updated 4.8 years ago by 43k • written 4.8 years ago by • 0
6
votes
4
replies
3.5k
views
confused with tximport counts abundance using salmon input
RNASeq tximport
2.8 years ago Al90 ▴ 10
1
vote
8
replies
3.4k
views
IgnoreTxVersion on Tximport not working
Tximport Salmon
5.3 years ago k1m ▴ 20
1
vote
5
replies
3.4k
views
tximport error with kallisto .h5 files
deseq2 kallisto tximport
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
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
1
vote
5
replies
3.2k
views
RNA-seq analysis on mouse data with human contamination in controls
rna-seq salmon tximport limma
updated 7.7 years ago by ★ 28k • written 7.7 years ago by ▴ 70
6
votes
7
replies
3.2k
views
edgeR + tximport: calcNormFactors and the usage of offsets
edgeR tximport differential expression
updated 25 days ago by 52k • written 4.7 years ago by ▴ 20
0
votes
6
replies
3.2k
views
Salmon, tximport and DeSeq2 for differential expression analysis of 3' biased data
tximport DESeq2 "tximport" deseq2 salmon
7.6 years ago sunil.mangalam • 0
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
1
vote
9
replies
3.0k
views
error in aSwitchlist (isoformswitchanalyzeR)
isoformswitchanalyzeR tximport rnaseq salmon
updated 5.8 years ago by ▴ 120 • written 5.8 years ago by • 0
0
votes
2
replies
3.0k
views
tximport ERROR : all(file.exists(files)) is not TRUE
Linux R tximport
2.9 years ago nakane_clan • 0
2
votes
7
replies
3.0k
views
tximport - using hg38 with RefSeq (NM) and Gene Symbol
salmon hg38 tximport tx2gene.csv
updated 7.9 years ago by 43k • written 7.9 years ago by • 0
0
votes
3
replies
3.0k
views
"lexical error: invalid char in json text" when using tximport
tximport salmon
updated 5.0 years ago by 43k • written 5.0 years ago by • 0
2
votes
19
replies
3.0k
views
tximport returns NA counts
tximport
7.2 years ago leonfodoulian • 0
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
A: DESeq2 interaction term
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.
Awards • All
Popular Question to ajglajd gajgflkadfj gl • 0
Popular Question to Robert Castelo ★ 3.4k
Popular Question to Robert Ivanek ▴ 750
Popular Question to shepherl 4.1k
Popular Question to Martin Morgan 25k
Locations • All
The city by the bay, 18 minutes ago
Denmark, 25 minutes ago
WEHI, Melbourne, Australia, 51 minutes ago
Belgium, 1 hour ago
Pittsburgh, United States, 4 hours ago
Traffic: 433 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6