Showing : tximport • reset
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Best tximport quant.genes.sf
tximport tximeta Bioconductor
updated 1 day ago by ★ 4.8k • written 2 days ago by • 0
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4
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1.2k
views
Error in H5Dclose(h5dataset) when trying to read in kallisto h5 files
tximport rhdf5
6 weeks ago Sofia • 0
0
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4
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591
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Using tximport for kallisto aligned TOIL data
kallisto tximport TOIL
9 weeks ago • updated 8 weeks ago Nicholas • 0
0
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11
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950
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Problems with oarfish + tximport + swish
fishpond tximport tximeta
updated 3 months ago by • 0 • written 3 months ago by • 0
1
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2
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846
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Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport DESeq2 GSVA
5 months ago georgii.vdovin • 0
4
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5
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1.0k
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DESeq Input from Salmon + tximport/tximeta
tximportData summarizeToGene tximport DESeq2 salmon
6 months ago LuciaNhu • 0
0
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2
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547
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How can I obtain DEGs that are resulted from using salmon in alignment-based mode or mapping-based mode?
tximport DESeq2
updated 7 months ago by 43k • written 7 months ago by • 0
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2
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528
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tximport data import
tximport
updated 8 months ago by 43k • written 8 months ago by • 0
1
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2
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1.1k
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How to use specific size factors and average transcript lengths from tximport in DESeq2?
DESeq2 tximport
9 months ago grothmn • 0
1
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2
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2.5k
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using tximport with STAR transcript-quantification output
tximport deseq2 STAR
updated 11 months ago by ▴ 40 • written 5.5 years ago by • 0
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4
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755
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Create count matrix from multible quant sf files from different directories
tximportData tximport salmon
11 months ago JG13 • 0
0
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2
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718
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edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
13 months ago Marianna ▴ 20
0
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2
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792
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Clarification on Library Size Normalization After Using tximport with countsFromAbundance="lengthScaledTPM"
tximport
updated 13 months ago by 43k • written 13 months ago by • 0
2
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1
reply
660
views
Creating data matrix in Deseq2 from tximport data invalid class SummarizedExperiment object
DESeq2 tximport
updated 14 months ago by ★ 4.8k • written 14 months ago by • 0
2
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3
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3.2k
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR tximport RNASeq DESeq2
updated 16 months ago by ★ 1.4k • written 17 months ago by • 0
0
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1
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883
views
tximport error with rsem files
rsem tximport
updated 17 months ago by ★ 4.8k • written 17 months ago by • 0
3
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2
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1.1k
views
tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
tximport DESeq2
updated 17 months ago by 68k • written 17 months ago by • 0
0
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3
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1.0k
views
Tximport Error - transcripts in quant files are not the same as tx2gene
salmon tximport deseq2
updated 19 months ago by 43k • written 19 months ago by • 0
10
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11
replies
3.1k
views
tximport error: vroom
tximport
updated 18 months ago by • 0 • written 19 months ago by ▴ 40
2
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3
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1.4k
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Import Salmon data with tximport and pool technical replicates
tximport edgeR
written 21 months ago by • 0
5
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13
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3.6k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport DESeq2
updated 19 months ago by 43k • written 20 months ago by • 0
2
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4
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1.8k
views
Handle zero effective gene length when tximport RSEM results
tximport edgeR
updated 20 months ago by 43k • written 21 months ago by ▴ 10
1
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2
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2.5k
views
IsoformSwitchAnalyzeR: What are the SV values created in design matrix?
salmon IsoformSwitchAnalyzeR tximport RNASeqData
updated 21 months ago by ▴ 120 • written 21 months ago by ▴ 10
2
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9
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2.0k
views
Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport tximportData DESeq2
22 months ago Ndimensional ▴ 20
0
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2
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1.1k
views
tximport error in reading salmon output files?
tximport tximportData
updated 15 months ago by • 0 • written 23 months ago by • 0
0
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1
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1.0k
views
Which file in tximport should I use for DESeq2 analysis?
tximport DESeq2
updated 24 months ago by 68k • written 24 months ago by • 0
2
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1
reply
1.2k
views
scaledTPM for DESeq2 using tximport
DESeq2 tximport
updated 2.0 years ago by 43k • written 2.0 years ago by • 0
3
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7
replies
1.7k
views
failed to use tximport for creating count matrix from kallisto
tximport kallisto
2.0 years ago Yijing • 0
0
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2
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1.4k
views
Error in H5Fopen
rhdf5 Rhdf5lib kallisto tximport
2.0 years ago Yijing • 0
1
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3
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1.4k
views
tximport error
tximport r
updated 2.1 years ago by 43k • written 2.1 years ago by • 0
0
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2
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1.6k
views
combining multiple salmon runs after tximport
tximport RNASeq salmon
updated 2.2 years ago by ★ 4.8k • written 2.2 years ago by • 0
1
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5
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1.8k
views
tximport: kallisto + GENCODE transcript sanitization
tximport
updated 2.2 years ago by 43k • written 2.2 years ago by ▴ 90
6
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10
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3.5k
views
Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
updated 12 months ago by • 0 • written 2.3 years ago by ▴ 10
0
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1
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1.1k
views
Is it possible to convert transcript-level to gene-level dataset to use it in DESeq2 ?
DESeq2 Transcriptomics tximport deseq txi
updated 2.3 years ago by ★ 1.6k • written 2.3 years ago by ▴ 10
0
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2
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1.4k
views
how to match salmon output to txname
GenomicFeatures tximport salmon
written 2.3 years ago by • 0
0
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1
reply
1.2k
views
Missing transcript
DESeq2 tximport salmon
updated 2.4 years ago by ★ 4.8k • written 2.4 years ago by • 0
2
votes
5
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2.4k
views
Normalizing Salmon output count data matrix using DESeq2
DESeq2 tximport counts Salmon
updated 14 months ago by 43k • written 2.4 years ago by • 0
0
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2
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1.2k
views
Differentially expression analysis of orthologous genes between two species
DESeq2 tximport
2.4 years ago Konstantinos • 0
2
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3
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1.9k
views
Error while reading rsem files in tximport
DESeq2 tximport rsem RNASeq tximportData
2.5 years ago • updated 2.4 years ago mohammedtoufiq91 ▴ 10
4
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3
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1.7k
views
tx2gene object trouble when working with kallisto and A.thaliana
tx2gene tximport Arabidopsis_thaliana kallisto
updated 2.5 years ago by 68k • written 2.5 years ago by ▴ 10
0
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1
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1.3k
views
Trouble with importing transcript counts with Salmon
Salmon tximport RNAseq EdgeR
updated 2.5 years ago by ★ 4.8k • written 2.5 years ago by • 0
1
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2
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1.2k
views
error loading kallisto output in tximport
file.exists false kallisto tximport
2.5 years ago cta • 0
2
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3
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2.3k
views
How to convert transcript counts to gene counts in R?
DESeq2 tximport
updated 20 days ago by • 0 • written 2.6 years ago by ▴ 50
3
votes
3
replies
1.6k
views
What is the correct way to import transcript abundances from 3' Quantseq results that calculated by kallisto?
tximport tximportData Quantseq kallisto
2.6 years ago • updated 2.5 years ago duhwa.lee • 0
1
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2
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2.4k
views
transcripts missing from tx2gene
tximport
2.6 years ago Erick • 0
0
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1
reply
992
views
tximport: not all(file.exists(files)) are true
tximport
updated 2.6 years ago by 43k • written 2.6 years ago by • 0
3
votes
1
reply
3.4k
views
Understanding tximport working with salmon outputs
Transcriptomics tximport
updated 2.7 years ago by ★ 4.8k • written 2.7 years ago by ▴ 10
3
votes
4
replies
2.2k
views
difference between txi$counts and txi$abundance when countsFromAbundance is true
RNAseq tximport
updated 2.7 years ago by ★ 4.8k • written 2.7 years ago by • 0
0
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3
replies
1.4k
views
tximport error
error tximport
updated 2.7 years ago by 43k • written 2.7 years ago by • 0
5
votes
6
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2.2k
views
Selecting individual samples from tximport and DGE matrix design with missing biological replicate
DESeq2 limma tximport
updated 2.7 years ago by 52k • written 2.7 years ago by • 0
50 results • Page 1 of 1
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Replies
Comment: How to extract coordinates of mismatches from a BAM file lodaded in as a GAlignm by Charles • 0
I am trying this but it is slow. ``` aln2mismatches <- function (gal) { gr <- GRanges(gal) irl <- cigarRangesAlongReferenceSpace(cigar…
Answer: DESeq2 Apeglm Coefficient Reordering / Log2FoldChange Comparison Change by James W. MacDonald 68k
Yes, you can simply flip the sign of the logFC to reverse the direction of the comparison.
Comment: Heatmap of a transformed deseq object with pheatmap by James W. MacDonald 68k
The argument for annotation_col is meant to be a `data.frame`, not a vector. The hint in the error is that it has the wrong number of dimen…
Comment: Heatmap of a transformed deseq object with pheatmap by caroline.zanchi • 0
I used this argument in the second paragraph of code forthe heatmap, this is wehre I got the message Error in `[.default`(annotation_col, c…
Answer: Heatmap of a transformed deseq object with pheatmap by James W. MacDonald 68k
Ah, yes. The non-ASCII character error. My favorite! Please note that `pheatmap` is not a Bioconductor package, so you should be asking …
Votes
Comment: Heatmap of a transformed deseq object with pheatmap
DESeq2: Question about the alpha in summary() and results()
Comment: How to load scRNA-seq data from GEO
limma correction for tumor purity
limma correction for tumor purity
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