Showing : tximport • reset
32
votes
16
replies
20k
views
difference among tximport scaledTPM, lengthScaledTPM and the original TPM output by salmon/kallisto
tximport deseq2 TPM RPKM rnaseq
updated 6.9 years ago by ▴ 20 • written 8.7 years ago by ▴ 200
0
votes
1
reply
14k
views
there is no "tx2gene.gencode.v27.csv" in tximportData
tximport
updated 6.9 years ago by 43k • written 6.9 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 7.1 years ago by 43k • written 7.1 years ago by ▴ 30
0
votes
5
replies
10k
views
tximport all(file.exists(files)) is not TRUE
bioconductor tximport rnaseq R
updated 12 months ago by • 0 • written 8.5 years ago by • 0
9
votes
2
replies
10k
views
Using RSEM with tximport and DESeq2
deseq2 tximport software error bug
updated 3.5 years ago by 43k • written 8.1 years ago by ▴ 10
1
vote
11
replies
8.0k
views
RNA Seq data analysis using Salmon and tximport
RNAseq tximport
7.5 years ago tanyabioinfo ▴ 20
3
votes
2
replies
7.4k
views
Non-integer counts from tximport OK for edgeR / DESeq2?
tximport edgeR DESeq2
updated 8.4 years ago by 43k • written 8.4 years ago by ★ 2.0k
7
votes
17
replies
6.2k
views
DESeqDataSetFromTximport: Error in checkSlotAssignment
deseq2 tximport
7.9 years ago JWCarlson ▴ 80
5
votes
9
replies
6.1k
views
Trouble with Tximport
tximport salmon
updated 8.9 years ago by 43k • written 8.9 years ago by ▴ 30
9
votes
11
replies
6.0k
views
Using 'tximport' library for downstream DGE after quantifying with Kallisto
tximport Kallisto rna-seq
updated 8.1 years ago by ▴ 20 • written 8.9 years ago by ▴ 10
3
votes
9
replies
5.9k
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
6.1 years ago • updated 6.0 years ago Leo K • 0
2
votes
4
replies
5.8k
views
tximport, Kallisto and Deseq2 (quick answer)
kallisto tximport deseq2 counts
5.9 years ago • updated 5.0 years ago Mozart ▴ 30
5
votes
5
replies
5.8k
views
tximport transcript missing
deseq2 salmon tximport
5.7 years ago mr6518849 ▴ 10
2
votes
2
replies
5.8k
views
Importing data into the DESeq2 pipeline using tximport
DESeq2 tximport
4.1 years ago Nikolay Ivanov • 0
6
votes
4
replies
5.4k
views
Is there any point to TMM-normalize TPM prior to limma-voom?
voom limma-voom tximport edger
updated 8.0 years ago by ★ 7.9k • written 8.0 years ago by ▴ 10
1
vote
3
replies
5.3k
views
PCA from TPM
pca tpm tximport
7.4 years ago tanyabioinfo ▴ 20
4
votes
7
replies
5.2k
views
Analyzing TCGA RSEM Data with DESeq2 downloaded from FireBrowse
deseq2 tximport tcga rsem firebrowse
updated 4.8 years ago by ★ 4.0k • written 4.8 years ago by • 0
4
votes
9
replies
5.1k
views
How to get DESeq2 sizefactors from data imported using tximport
deseq2 sailfish tximport
updated 22 months ago by • 0 • written 7.7 years ago by • 0
0
votes
3
replies
4.9k
views
Create Ensembl transcript to gene IDs table with R ensembldb package for tximport
ensembldb tximport salmon
updated 6.8 years ago by ★ 2.1k • written 6.8 years ago by ▴ 30
2
votes
8
replies
4.7k
views
Which R version is needed for tximport package?
tximport package R version install tximport
4.6 years ago harelarik ▴ 60
7
votes
8
replies
4.7k
views
R failing to load genome files from EnsDb.Hsapiens.v86
tximport ensembldb EnsDB.hsapiens.v86
updated 6.2 years ago by 0 • written 6.3 years ago by ▴ 20
8
votes
12
replies
4.5k
views
How to create tx2gene data.frame when there's no TxDb object for the organism you are working with.
tximport deseq2 annotationdbi
updated 7.5 years ago by ★ 2.1k • written 7.5 years ago by • 0
4
votes
3
replies
4.5k
views
txtimportData installation on R version 3.3.0 (2016-05-03)
tximport deseq2
8.7 years ago jarod_v6@libero.it ▴ 40
5
votes
6
replies
4.4k
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 5.4 years ago by ★ 3.4k • written 5.4 years ago by ▴ 80
3
votes
4
replies
4.4k
views
Importing RSEM transcript-level data using tximport
tximport rsem
updated 7.3 years ago by 43k • written 7.3 years ago by ▴ 10
2
votes
5
replies
4.0k
views
unable to get tximport to work on data from kallisto
tximport kallisto
updated 7.9 years ago by ★ 13k • written 7.9 years ago by ▴ 10
16
votes
25
replies
4.0k
views
dtuScaledTPM vs lengthScaledTPM in DTU analysis
tximport dtu salmon TPM rnaseqDTU
written 6.0 years ago by ▴ 60
9
votes
4
replies
4.0k
views
GC/length bias correction in gene expression quantification - Is CQN necessary if using Salmon --GCBias option?
salmon cqn tximport deseq2 rnaseq
updated 8.0 years ago by 43k • written 8.1 years ago by ▴ 30
2
votes
18
replies
4.0k
views
Using tximport on rsem files produces error while trying to read in files
R tximport rnaseq tpm rsem
7.0 years ago stephan.emmrich ▴ 10
5
votes
9
replies
4.0k
views
Correct version of EnsDb.Hsapiens for ensembl transcriptome
ensembldb ensembl release rnaseq salmon tximport
7.1 years ago emmak ▴ 20
0
votes
4
replies
3.9k
views
Tutorial: Importing multiple .h5 files using tximport
tximport Tutorial
updated 6.9 years ago by ★ 13k • written 6.9 years ago by ▴ 10
4
votes
3
replies
3.9k
views
tximport error: all(names(aveLengthSampGene) == rownames(lengthMat)) is not TRUE
tximport salmon R bioconductor
updated 3.2 years ago by • 0 • written 7.7 years ago by • 0
6
votes
4
replies
3.8k
views
confused with tximport counts abundance using salmon input
RNASeq tximport
2.9 years ago Al90 ▴ 10
6
votes
3
replies
3.8k
views
Full length single-cell RNA-seq - tximport output for downstream analysis
tximport Seurat Smart-Seq Smart-Seq2
updated 4.7 years ago by 43k • written 4.7 years ago by ▴ 40
2
votes
6
replies
3.7k
views
Subsetting a tximport object
tximport
written 7.0 years ago by • 0
1
vote
5
replies
3.7k
views
tximport using for data generated from other tools
tximport salmon eXpress
updated 6.9 years ago by 43k • written 7.8 years ago by • 0
1
vote
5
replies
3.6k
views
tximport error: all(txId == raw[[txIdCol]]) is not TRUE
tximport
updated 20 months ago by 43k • written 3.4 years ago by • 0
1
vote
9
replies
3.6k
views
Importing Kallisto counts with tximport
tximport Kallisto H5Fopen
updated 4.9 years ago by 43k • written 4.9 years ago by • 0
1
vote
8
replies
3.6k
views
IgnoreTxVersion on Tximport not working
Tximport Salmon
5.5 years ago k1m ▴ 20
1
vote
5
replies
3.4k
views
tximport error with kallisto .h5 files
deseq2 kallisto tximport
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
5
votes
5
replies
3.4k
views
Problem with tximport(reader = read_tsv) and workaround
tximport readr read_tsv
updated 8.5 years ago by 43k • written 8.5 years ago by ★ 2.0k
6
votes
7
replies
3.4k
views
edgeR + tximport: calcNormFactors and the usage of offsets
edgeR tximport differential expression
updated 11 weeks ago by 52k • written 4.8 years ago by ▴ 20
1
vote
5
replies
3.3k
views
RNA-seq analysis on mouse data with human contamination in controls
rna-seq salmon tximport limma
updated 7.9 years ago by ★ 28k • written 7.9 years ago by ▴ 70
0
votes
6
replies
3.2k
views
Salmon, tximport and DeSeq2 for differential expression analysis of 3' biased data
tximport DESeq2 "tximport" deseq2 salmon
7.8 years ago sunil.mangalam • 0
4
votes
14
replies
3.2k
views
running tximport for salmon quants
tximport readr
updated 8.8 years ago by 43k • written 8.8 years ago by • 0
5
votes
13
replies
3.2k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport DESeq2
updated 17 months ago by 43k • written 18 months ago by • 0
6
votes
10
replies
3.2k
views
Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
updated 11 months ago by • 0 • written 2.1 years ago by ▴ 10
0
votes
2
replies
3.1k
views
tximport ERROR : all(file.exists(files)) is not TRUE
Linux R tximport
3.1 years ago nakane_clan • 0
1
vote
9
replies
3.1k
views
error in aSwitchlist (isoformswitchanalyzeR)
isoformswitchanalyzeR tximport rnaseq salmon
updated 6.0 years ago by ▴ 120 • written 6.0 years ago by • 0
2
votes
7
replies
3.1k
views
tximport - using hg38 with RefSeq (NM) and Gene Symbol
salmon hg38 tximport tx2gene.csv
updated 8.0 years ago by 43k • written 8.0 years ago by • 0
50 results • Page 1 of 1
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Comment: Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with by Gordon Smyth 52k
I generally recommend `block=individual` for unbalanced designs, to recover information from incomplete blocks. I would only be disuaded fr…
Comment: Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with by Devin ▴ 10
Thank you, Gordon, for your responses to all of my questions. For analysis A), in the case when a patient has either a missing timepoint or…
Comment: Using TPM from tximport of Salmon output for singscore by Kent • 0
Thanks Michael. Just out of curiosity, would you also use the same technique for things like clustering analysis or when looking at the abn…
Comment: GAGE kegg.gsets() self-signed certificate error by Lucas • 0
Hello, I ended up solving the issue by using the first strategy: Disable the SSL certificate Verification. I used the following code to …
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Thank you for your answer James. I have to disagree though, at the SGD webpage you posted there is no indication that "GO:0045719 - negati…
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Comment: Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with
Answer: Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with
Answer: Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with
Answer: Using TPM from tximport of Salmon output for singscore
Comment: Using TPM from tximport of Salmon output for singscore
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