Showing : txImport • reset
28
votes
16
replies
12k
views
difference among tximport scaledTPM, lengthScaledTPM and the original TPM output by salmon/kallisto
tximport deseq2 TPM RPKM rnaseq
updated 4.1 years ago by ▴ 10 • written 5.9 years ago by ▴ 190
5
votes
10
replies
6.8k
views
Constructing tx2gene for Salmon txImport Quantification using Gencode Mouse Transcript Annotation
Michael Love Salmon tximport tx2gene
updated 4.2 years ago by 37k • written 4.3 years ago by ▴ 30
0
votes
4
replies
5.7k
views
tximport all(file.exists(files)) is not TRUE
bioconductor tximport rnaseq R
5.7 years ago ctl • 0
1
vote
11
replies
5.5k
views
RNA Seq data analysis using Salmon and tximport
RNAseq tximport
4.6 years ago tanyabioinfo ▴ 20
6
votes
2
replies
5.3k
views
Using RSEM with tximport and DESeq2
deseq2 tximport software error bug
updated 8 months ago by 37k • written 5.3 years ago by • 0
3
votes
2
replies
4.9k
views
Non-integer counts from tximport OK for edgeR / DESeq2?
tximport edgeR DESeq2
updated 5.6 years ago by 37k • written 5.6 years ago by ★ 2.0k
9
votes
11
replies
4.6k
views
Using 'tximport' library for downstream DGE after quantifying with Kallisto
tximport Kallisto rna-seq
updated 5.2 years ago by ▴ 20 • written 6.1 years ago by ▴ 10
7
votes
17
replies
4.2k
views
DESeqDataSetFromTximport: Error in checkSlotAssignment
deseq2 tximport
5.1 years ago JWCarlson ▴ 80
5
votes
9
replies
3.7k
views
Trouble with Tximport
tximport salmon
updated 6.1 years ago by 37k • written 6.1 years ago by ▴ 30
6
votes
4
replies
3.6k
views
Is there any point to TMM-normalize TPM prior to limma-voom?
voom limma-voom tximport edger
updated 5.2 years ago by 7.8k • written 5.2 years ago by ▴ 10
4
votes
3
replies
3.6k
views
txtimportData installation on R version 3.3.0 (2016-05-03)
tximport deseq2
5.9 years ago jarod_v6@libero.it ▴ 40
4
votes
7
replies
2.8k
views
How to get DESeq2 sizefactors from data imported using tximport
deseq2 sailfish tximport
updated 4.9 years ago by 37k • written 4.9 years ago by • 0
2
votes
5
replies
2.7k
views
unable to get tximport to work on data from kallisto
tximport kallisto
updated 5.0 years ago by 13k • written 5.0 years ago by ▴ 10
5
votes
5
replies
2.5k
views
tximport transcript missing
deseq2 salmon tximport
2.8 years ago mr6518849 ▴ 10
1
vote
3
replies
2.5k
views
PCA from TPM
pca tpm tximport
4.6 years ago tanyabioinfo ▴ 20
7
votes
4
replies
2.5k
views
GC/length bias correction in gene expression quantification - Is CQN necessary if using Salmon --GCBias option?
salmon cqn tximport deseq2 rnaseq
updated 5.2 years ago by 37k • written 5.2 years ago by ▴ 20
8
votes
12
replies
2.5k
views
How to create tx2gene data.frame when there's no TxDb object for the organism you are working with.
tximport deseq2 annotationdbi
updated 4.7 years ago by ★ 1.9k • written 4.7 years ago by • 0
0
votes
6
replies
2.4k
views
Salmon, tximport and DeSeq2 for differential expression analysis of 3' biased data
tximport DESeq2 "tximport" deseq2 salmon
5.0 years ago sunil.mangalam • 0
1
vote
5
replies
2.4k
views
tximport using for data generated from other tools
tximport salmon eXpress
updated 4.0 years ago by 37k • written 5.0 years ago by • 0
0
votes
1
reply
2.4k
views
there is no "tx2gene.gencode.v27.csv" in tximportData
tximport
updated 4.0 years ago by 37k • written 4.0 years ago by • 0
3
votes
9
replies
2.3k
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
3.2 years ago Leo K • 0
1
vote
18
replies
2.3k
views
Using tximport on rsem files produces error while trying to read in files
R tximport rnaseq tpm rsem
4.2 years ago stephan.emmrich • 0
3
votes
1
reply
2.3k
views
Gene level exploratory data analysis from tximport results
tximport edgeR DESeq2
updated 5.9 years ago by 37k • written 5.9 years ago by 13k
3
votes
4
replies
2.2k
views
Importing RSEM transcript-level data using tximport
tximport rsem
updated 4.5 years ago by 37k • written 4.5 years ago by ▴ 10
4
votes
3
replies
2.1k
views
tximport error: all(names(aveLengthSampGene) == rownames(lengthMat)) is not TRUE
tximport salmon R bioconductor
updated 4 months ago by • 0 • written 4.9 years ago by • 0
2
votes
4
replies
2.1k
views
tximport, Kallisto and Deseq2 (quick answer)
kallisto tximport deseq2 counts
3.1 years ago • updated 2.2 years ago Mozart ▴ 20
5
votes
9
replies
2.1k
views
Correct version of EnsDb.Hsapiens for ensembl transcriptome
ensembldb ensembl release rnaseq salmon tximport
4.3 years ago emmak ▴ 20
7
votes
8
replies
2.1k
views
R failing to load genome files from EnsDb.Hsapiens.v86
tximport ensembldb EnsDB.hsapiens.v86
updated 3.4 years ago by 0 • written 3.5 years ago by ▴ 20
0
votes
3
replies
2.0k
views
Create Ensembl transcript to gene IDs table with R ensembldb package for tximport
ensembldb tximport salmon
updated 4.0 years ago by ★ 1.9k • written 4.0 years ago by ▴ 30
4
votes
14
replies
2.0k
views
running tximport for salmon quants
tximport readr
updated 5.9 years ago by 37k • written 5.9 years ago by • 0
5
votes
5
replies
2.0k
views
Problem with tximport(reader = read_tsv) and workaround
tximport readr read_tsv
updated 5.7 years ago by 37k • written 5.7 years ago by ★ 2.0k
2
votes
3
replies
2.0k
views
Getting between sample/within sample normalized gene expression values from DESeq2
rnaseq deseq2 tximport salmon normalization
updated 5.0 years ago by 37k • written 5.0 years ago by • 0
0
votes
4
replies
2.0k
views
Tutorial: Importing multiple .h5 files using tximport
tximport Tutorial
updated 4.0 years ago by 13k • written 4.1 years ago by ▴ 10
3
votes
5
replies
1.9k
views
txImport: a gene seems missing from the sample data
txImportData txImport
updated 16 months ago by 59k • written 5.2 years ago by • 0
2
votes
7
replies
1.9k
views
tximport - using hg38 with RefSeq (NM) and Gene Symbol
salmon hg38 tximport tx2gene.csv
updated 5.2 years ago by 37k • written 5.2 years ago by • 0
3
votes
11
replies
1.8k
views
should I use rsem's summary to genes or tximport's?
tximport
updated 6.0 years ago by 37k • written 6.0 years ago by ▴ 10
1
vote
4
replies
1.7k
views
If transcript-to-gene conversion is needed in kallisto > tximport > DESeq2 pipeline
deseq2 rnaseq kallisto tximport
updated 4.2 years ago by 37k • written 4.2 years ago by • 0
3
votes
5
replies
1.7k
views
DESeqDataSetFromTximport with kallisto abundances.
deseq2 tximport
updated 4.6 years ago by • 0 • written 5.0 years ago by ▴ 30
0
votes
7
replies
1.7k
views
Error reading kallisto files using tximport for cross species RNA-Seq analysis
kallisto tximport RNA-Seq across species
updated 6 months ago by • 0 • written 5.0 years ago by ▴ 40
1
vote
5
replies
1.7k
views
tximport error with kallisto .h5 files
deseq2 kallisto tximport
updated 3.4 years ago by 37k • written 3.4 years ago by • 0
1
vote
5
replies
1.6k
views
RNA-seq analysis on mouse data with human contamination in controls
rna-seq salmon tximport limma
updated 5.1 years ago by ★ 27k • written 5.1 years ago by ▴ 60
2
votes
19
replies
1.6k
views
tximport returns NA counts
tximport
4.5 years ago leonfodoulian • 0
2
votes
6
replies
1.6k
views
Subsetting a tximport object
tximport
updated 4.2 years ago by • 0 • written 4.2 years ago by • 0
0
votes
3
replies
1.6k
views
(very) conflicting results with DESeq2 between versions
deseq2 tximport rnaseq kallisto R
updated 5.0 years ago by 37k • written 5.0 years ago by • 0
2
votes
8
replies
1.6k
views
Which R version is needed for tximport package?
tximport package R version install tximport
21 months ago harelarik ▴ 50
5
votes
6
replies
1.5k
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 2.6 years ago by ★ 2.9k • written 2.6 years ago by ▴ 80
2
votes
4
replies
1.5k
views
tximport of kallisto files
tximport deseq2 kallisto
updated 4.5 years ago by 37k • written 4.5 years ago by • 0
1
vote
4
replies
1.5k
views
tximport error reading salmon quantification files...
tximport salmon
updated 5.2 years ago by 59k • written 5.2 years ago by ▴ 20
1
vote
3
replies
1.5k
views
DESeq2 size factors estimation after RSEM quantification
deseq2 tximport rsem estimatesizefactors
6.0 years ago Hugo Varet ▴ 80
0
votes
6
replies
1.5k
views
tximport allfile.exists(files)--> FALSE
tximport
updated 3.8 years ago by 59k • written 3.8 years ago by • 0
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Comment: Error in h(simpleError(msg, call)) : when calling makeOrgPackagefromNCBI() by Lan Anh • 0
Hello, Sorry for the late answer, I called several packages after my error and I do not know how it worked after that. Thank you for the h…
Comment: LogFC values in edgeR - w/wo intercept by JK Kim • 0
Thanks, Dr. Smyth!
Comment: LogFC values in edgeR - w/wo intercept by JK Kim • 0
Oops. I just corrected the URL. Thank you Dr. Smyth.
Comment: Fail to run RupRadar by Qingwei • 0
Dear Sergi, Yeah, it works. ```r dm <- analyzeDuprates(bamDuprm,gtf,stranded,paired,threads, GTF.featureType="cDNA_match", GTF.attrType="ID…
Comment: LogFC values in edgeR - w/wo intercept by Gordon Smyth 45k
The link you've entered for "A guide to creating design matrices for gene expression experiments" doesn't work. Could you please correct th…
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Comment: LogFC values in edgeR - w/wo intercept
Answer: LogFC values in edgeR - w/wo intercept
Answer: LogFC values in edgeR - w/wo intercept
Answer: broken chain import in liftOver
Answer: toGRanges help!
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