Showing : tximport • reset
32
votes
16
replies
17k
views
difference among tximport scaledTPM, lengthScaledTPM and the original TPM output by salmon/kallisto
tximport deseq2 TPM RPKM rnaseq
updated 6.0 years ago by ▴ 20 • written 7.8 years ago by ▴ 190
0
votes
1
reply
12k
views
there is no "tx2gene.gencode.v27.csv" in tximportData
tximport
updated 5.9 years ago by 41k • written 5.9 years ago by • 0
5
votes
10
replies
11k
views
Constructing tx2gene for Salmon txImport Quantification using Gencode Mouse Transcript Annotation
Michael Love Salmon tximport tx2gene
updated 6.1 years ago by 41k • written 6.1 years ago by ▴ 30
0
votes
5
replies
9.2k
views
tximport all(file.exists(files)) is not TRUE
bioconductor tximport rnaseq R
updated 27 days ago by • 0 • written 7.6 years ago by • 0
9
votes
2
replies
8.7k
views
Using RSEM with tximport and DESeq2
deseq2 tximport software error bug
updated 2.6 years ago by 41k • written 7.2 years ago by ▴ 10
1
vote
11
replies
7.1k
views
RNA Seq data analysis using Salmon and tximport
RNAseq tximport
6.5 years ago tanyabioinfo ▴ 20
3
votes
2
replies
6.6k
views
Non-integer counts from tximport OK for edgeR / DESeq2?
tximport edgeR DESeq2
updated 7.5 years ago by 41k • written 7.5 years ago by ★ 2.0k
9
votes
11
replies
5.5k
views
Using 'tximport' library for downstream DGE after quantifying with Kallisto
tximport Kallisto rna-seq
updated 7.1 years ago by ▴ 20 • written 8.0 years ago by ▴ 10
7
votes
17
replies
5.4k
views
DESeqDataSetFromTximport: Error in checkSlotAssignment
deseq2 tximport
7.0 years ago JWCarlson ▴ 80
5
votes
9
replies
5.3k
views
Trouble with Tximport
tximport salmon
updated 8.0 years ago by 41k • written 8.0 years ago by ▴ 30
3
votes
9
replies
4.8k
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
5.1 years ago Leo K • 0
5
votes
5
replies
4.8k
views
tximport transcript missing
deseq2 salmon tximport
4.7 years ago mr6518849 ▴ 10
6
votes
4
replies
4.7k
views
Is there any point to TMM-normalize TPM prior to limma-voom?
voom limma-voom tximport edger
updated 7.1 years ago by ★ 7.9k • written 7.1 years ago by ▴ 10
2
votes
4
replies
4.5k
views
tximport, Kallisto and Deseq2 (quick answer)
kallisto tximport deseq2 counts
5.0 years ago • updated 4.1 years ago Mozart ▴ 30
1
vote
2
replies
4.5k
views
Importing data into the DESeq2 pipeline using tximport
DESeq2 tximport
3.2 years ago Nikolay Ivanov • 0
1
vote
3
replies
4.4k
views
PCA from TPM
pca tpm tximport
6.5 years ago tanyabioinfo ▴ 20
4
votes
9
replies
4.3k
views
How to get DESeq2 sizefactors from data imported using tximport
deseq2 sailfish tximport
updated 10 months ago by • 0 • written 6.8 years ago by • 0
0
votes
3
replies
4.3k
views
Create Ensembl transcript to gene IDs table with R ensembldb package for tximport
ensembldb tximport salmon
updated 5.9 years ago by ★ 2.0k • written 5.9 years ago by ▴ 30
4
votes
3
replies
4.2k
views
txtimportData installation on R version 3.3.0 (2016-05-03)
tximport deseq2
7.8 years ago jarod_v6@libero.it ▴ 40
4
votes
7
replies
3.9k
views
Analyzing TCGA RSEM Data with DESeq2 downloaded from FireBrowse
deseq2 tximport tcga rsem firebrowse
updated 3.9 years ago by ★ 3.9k • written 3.9 years ago by • 0
8
votes
12
replies
3.8k
views
How to create tx2gene data.frame when there's no TxDb object for the organism you are working with.
tximport deseq2 annotationdbi
updated 6.6 years ago by ★ 2.0k • written 6.6 years ago by • 0
7
votes
8
replies
3.7k
views
R failing to load genome files from EnsDb.Hsapiens.v86
tximport ensembldb EnsDB.hsapiens.v86
updated 5.3 years ago by 0 • written 5.4 years ago by ▴ 20
3
votes
4
replies
3.6k
views
Importing RSEM transcript-level data using tximport
tximport rsem
updated 6.4 years ago by 41k • written 6.4 years ago by ▴ 10
2
votes
8
replies
3.6k
views
Which R version is needed for tximport package?
tximport package R version install tximport
3.6 years ago harelarik ▴ 60
2
votes
5
replies
3.6k
views
unable to get tximport to work on data from kallisto
tximport kallisto
updated 6.9 years ago by ★ 13k • written 6.9 years ago by ▴ 10
5
votes
9
replies
3.4k
views
Correct version of EnsDb.Hsapiens for ensembl transcriptome
ensembldb ensembl release rnaseq salmon tximport
6.2 years ago emmak ▴ 20
2
votes
18
replies
3.4k
views
Using tximport on rsem files produces error while trying to read in files
R tximport rnaseq tpm rsem
6.1 years ago • updated 6.0 years ago stephan.emmrich ▴ 10
4
votes
3
replies
3.4k
views
tximport error: all(names(aveLengthSampGene) == rownames(lengthMat)) is not TRUE
tximport salmon R bioconductor
updated 2.3 years ago by • 0 • written 6.8 years ago by • 0
9
votes
4
replies
3.3k
views
GC/length bias correction in gene expression quantification - Is CQN necessary if using Salmon --GCBias option?
salmon cqn tximport deseq2 rnaseq
updated 7.1 years ago by 41k • written 7.1 years ago by ▴ 30
5
votes
6
replies
3.3k
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 4.5 years ago by ★ 3.2k • written 4.5 years ago by ▴ 80
0
votes
4
replies
3.2k
views
Tutorial: Importing multiple .h5 files using tximport
tximport Tutorial
updated 5.9 years ago by ★ 13k • written 5.9 years ago by ▴ 10
1
vote
5
replies
3.1k
views
tximport using for data generated from other tools
tximport salmon eXpress
updated 5.9 years ago by 41k • written 6.9 years ago by • 0
5
votes
3
replies
3.0k
views
Full length single-cell RNA-seq - tximport output for downstream analysis
tximport Seurat Smart-Seq Smart-Seq2
updated 3.8 years ago by 41k • written 3.8 years ago by ▴ 40
2
votes
6
replies
2.9k
views
Subsetting a tximport object
tximport
written 6.1 years ago by • 0
16
votes
25
replies
2.9k
views
dtuScaledTPM vs lengthScaledTPM in DTU analysis
tximport dtu salmon TPM rnaseqDTU
written 5.0 years ago by ▴ 60
1
vote
9
replies
2.9k
views
Importing Kallisto counts with tximport
tximport Kallisto H5Fopen
updated 4.0 years ago by 41k • written 4.0 years ago by • 0
1
vote
5
replies
2.9k
views
tximport error with kallisto .h5 files
deseq2 kallisto tximport
updated 5.3 years ago by 41k • written 5.3 years ago by • 0
5
votes
5
replies
2.9k
views
Problem with tximport(reader = read_tsv) and workaround
tximport readr read_tsv
updated 7.6 years ago by 41k • written 7.6 years ago by ★ 2.0k
0
votes
6
replies
2.8k
views
Salmon, tximport and DeSeq2 for differential expression analysis of 3' biased data
tximport DESeq2 "tximport" deseq2 salmon
6.9 years ago sunil.mangalam • 0
4
votes
14
replies
2.8k
views
running tximport for salmon quants
tximport readr
updated 7.8 years ago by 41k • written 7.8 years ago by • 0
1
vote
8
replies
2.8k
views
IgnoreTxVersion on Tximport not working
Tximport Salmon
4.6 years ago k1m ▴ 20
1
vote
5
replies
2.8k
views
tximport error: all(txId == raw[[txIdCol]]) is not TRUE
tximport
updated 9 months ago by 41k • written 2.5 years ago by • 0
3
votes
5
replies
2.7k
views
txImport: a gene seems missing from the sample data
txImportData txImport
updated 3.2 years ago by 65k • written 7.1 years ago by • 0
2
votes
19
replies
2.6k
views
tximport returns NA counts
tximport
6.4 years ago leonfodoulian • 0
3
votes
1
reply
2.6k
views
Gene level exploratory data analysis from tximport results
tximport edgeR DESeq2
updated 7.8 years ago by 41k • written 7.8 years ago by ★ 13k
2
votes
7
replies
2.6k
views
tximport - using hg38 with RefSeq (NM) and Gene Symbol
salmon hg38 tximport tx2gene.csv
updated 7.1 years ago by 41k • written 7.1 years ago by • 0
1
vote
5
replies
2.6k
views
RNA-seq analysis on mouse data with human contamination in controls
rna-seq salmon tximport limma
updated 7.0 years ago by ★ 28k • written 7.0 years ago by ▴ 70
3
votes
11
replies
2.6k
views
should I use rsem's summary to genes or tximport's?
tximport
updated 7.9 years ago by 41k • written 7.9 years ago by ▴ 10
0
votes
3
replies
2.5k
views
"lexical error: invalid char in json text" when using tximport
tximport salmon
updated 4.2 years ago by 41k • written 4.2 years ago by • 0
1
vote
4
replies
2.5k
views
If transcript-to-gene conversion is needed in kallisto > tximport > DESeq2 pipeline
deseq2 rnaseq kallisto tximport
updated 6.1 years ago by 41k • written 6.1 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: what is the sampleFiles by James W. MacDonald 65k
I don't see any sampleFiles argument for any function in that package. Ideally you would at least tell us what function you are using.
Comment: Interaction Terms in DESeq2 - Shrinkage by Michael Love 41k
Yes, apeglm requires relevel and nbinomWaldTest to generate the coefficient estimate and its SE. Alternatively you can use ashr with a con…
Comment: A ComBat-seq issue: the covariates are confounded by schlumbohm • 0
Dear ATpoint, thank you for the comment. I did correct the question. For the group, I did accidentally share the input for all three batch…
Comment: Memory errors using read.bismark? by Peter Hickey ▴ 690
If you process serially (i.e. with `BPPARAM = SerialParam()`) then you might be okay. The final object will be on the order of 250 GB in-me…
Comment: Memory errors using read.bismark? by Juan Higareda • 0
Thanks for the answer. Actually, processing one file and keeping it in memory wasn't the problem, is more processing all the 15 files to bu…
Votes
Comment: Not fully paired differential gene expression analysis
Comment: [DiffBind] Obtaining normalization factors
Answer: ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with var
Comment: Not fully paired differential gene expression analysis
Answer: GSVA error
Awards • All
Popular Question to paria.alipour • 0
Popular Question to Eman • 0
Popular Question to James W. MacDonald 65k
Scholar to nhaus ▴ 30
Popular Question to shepherl 3.8k
Locations • All
France, just now
Switzerland, 1 minute ago
France, 13 minutes ago
United Kingdom, 15 minutes ago
France, 19 minutes ago
Traffic: 770 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