Showing : Tximport • reset
0
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1
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592
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discrepancy in IDs from file and tx2gene (IDs don't match)
tximport DESeq2
updated 6 months ago by 68k • written 6 months ago by • 0
0
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1
reply
775
views
Which GTF file to use for creation of tx2gene files?
tximport
updated 7 months ago by 43k • written 7 months ago by • 0
0
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3
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1.1k
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Many transcripts missing from tx2gene created from Ensembl GTF file
kallisto tximport ensembl
updated 7 months ago by • 0 • written 7 months ago by • 0
0
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1
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517
views
Best tximport quant.genes.sf
tximport tximeta Bioconductor
updated 8 months ago by ★ 5.0k • written 8 months ago by • 0
0
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4
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1.6k
views
Error in H5Dclose(h5dataset) when trying to read in kallisto h5 files
tximport rhdf5
10 months ago Sofia • 0
0
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4
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937
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Using tximport for kallisto aligned TOIL data
kallisto tximport TOIL
10 months ago Nicholas • 0
0
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11
replies
1.6k
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Problems with oarfish + tximport + swish
fishpond tximport tximeta
updated 12 months ago by • 0 • written 12 months ago by • 0
1
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2
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1.3k
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Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport DESeq2 GSVA
13 months ago georgii.vdovin • 0
4
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5
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1.5k
views
DESeq Input from Salmon + tximport/tximeta
tximportData summarizeToGene tximport DESeq2 salmon
14 months ago LuciaNhu • 0
0
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2
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815
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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 16 months ago by 43k • written 16 months ago by • 0
0
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2
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804
views
tximport data import
tximport
updated 16 months ago by 43k • written 16 months ago by • 0
1
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2
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1.4k
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How to use specific size factors and average transcript lengths from tximport in DESeq2?
DESeq2 tximport
18 months ago grothmn • 0
1
vote
2
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3.0k
views
using tximport with STAR transcript-quantification output
tximport deseq2 STAR
updated 20 months ago by ▴ 40 • written 6.2 years ago by • 0
0
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4
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1.0k
views
Create count matrix from multible quant sf files from different directories
tximportData tximport salmon
20 months ago JG13 • 0
0
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2
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1.0k
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edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
22 months ago Marianna ▴ 20
0
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2
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1.2k
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Clarification on Library Size Normalization After Using tximport with countsFromAbundance="lengthScaledTPM"
tximport
updated 22 months ago by 43k • written 22 months ago by • 0
2
votes
1
reply
863
views
Creating data matrix in Deseq2 from tximport data invalid class SummarizedExperiment object
DESeq2 tximport
updated 22 months ago by ★ 5.0k • written 22 months ago by • 0
2
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3
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3.9k
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR tximport RNASeq DESeq2
updated 2.1 years ago by ★ 1.4k • written 2.1 years ago by • 0
0
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1
reply
1.2k
views
tximport error with rsem files
rsem tximport
updated 2.1 years ago by ★ 5.0k • written 2.1 years ago by • 0
3
votes
2
replies
1.4k
views
tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
tximport DESeq2
updated 2.2 years ago by 68k • written 2.2 years ago by • 0
0
votes
3
replies
1.4k
views
Tximport Error - transcripts in quant files are not the same as tx2gene
salmon tximport deseq2
updated 2.3 years ago by 43k • written 2.3 years ago by • 0
10
votes
11
replies
3.8k
views
tximport error: vroom
tximport
updated 2.3 years ago by • 0 • written 2.3 years ago by ▴ 40
2
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3
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1.7k
views
Import Salmon data with tximport and pool technical replicates
tximport edgeR
written 2.4 years ago by • 0
5
votes
13
replies
4.9k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport DESeq2
updated 2.3 years ago by 43k • written 2.4 years ago by • 0
2
votes
4
replies
2.1k
views
Handle zero effective gene length when tximport RSEM results
tximport edgeR
updated 2.4 years ago by 43k • written 2.4 years ago by ▴ 10
1
vote
2
replies
2.9k
views
IsoformSwitchAnalyzeR: What are the SV values created in design matrix?
salmon IsoformSwitchAnalyzeR tximport RNASeqData
updated 2.5 years ago by ▴ 120 • written 2.5 years ago by ▴ 10
2
votes
9
replies
2.6k
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Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport tximportData DESeq2
2.6 years ago Ndimensional ▴ 20
0
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2
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1.3k
views
tximport error in reading salmon output files?
tximport tximportData
updated 24 months ago by • 0 • written 2.6 years ago by • 0
0
votes
1
reply
1.2k
views
Which file in tximport should I use for DESeq2 analysis?
tximport DESeq2
updated 2.7 years ago by 68k • written 2.7 years ago by • 0
2
votes
1
reply
1.5k
views
scaledTPM for DESeq2 using tximport
DESeq2 tximport
updated 2.7 years ago by 43k • written 2.7 years ago by • 0
3
votes
7
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2.1k
views
failed to use tximport for creating count matrix from kallisto
tximport kallisto
2.7 years ago Yijing • 0
0
votes
2
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1.7k
views
Error in H5Fopen
rhdf5 Rhdf5lib kallisto tximport
2.8 years ago • updated 2.7 years ago Yijing • 0
1
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3
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1.7k
views
tximport error
tximport r
updated 2.8 years ago by 43k • written 2.8 years ago by • 0
0
votes
2
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1.8k
views
combining multiple salmon runs after tximport
tximport RNASeq salmon
updated 2.9 years ago by ★ 5.0k • written 2.9 years ago by • 0
1
vote
5
replies
2.2k
views
tximport: kallisto + GENCODE transcript sanitization
tximport
updated 2.9 years ago by 43k • written 3.0 years ago by ▴ 90
6
votes
10
replies
4.6k
views
Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
updated 21 months ago by • 0 • written 3.0 years ago by ▴ 10
0
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1
reply
1.3k
views
Is it possible to convert transcript-level to gene-level dataset to use it in DESeq2 ?
DESeq2 Transcriptomics tximport deseq txi
updated 3.0 years ago by ★ 1.6k • written 3.0 years ago by ▴ 10
0
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2
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1.6k
views
how to match salmon output to txname
GenomicFeatures tximport salmon
written 3.1 years ago by • 0
0
votes
1
reply
1.5k
views
Missing transcript
DESeq2 tximport salmon
updated 3.1 years ago by ★ 5.0k • written 3.1 years ago by • 0
2
votes
5
replies
2.9k
views
Normalizing Salmon output count data matrix using DESeq2
DESeq2 tximport counts Salmon
updated 23 months ago by 43k • written 3.1 years ago by • 0
0
votes
2
replies
1.5k
views
Differentially expression analysis of orthologous genes between two species
DESeq2 tximport
3.2 years ago Konstantinos • 0
2
votes
3
replies
2.3k
views
Error while reading rsem files in tximport
DESeq2 tximport rsem RNASeq tximportData
3.2 years ago mohammedtoufiq91 ▴ 10
4
votes
3
replies
2.0k
views
tx2gene object trouble when working with kallisto and A.thaliana
tx2gene tximport Arabidopsis_thaliana kallisto
updated 3.2 years ago by 68k • written 3.2 years ago by ▴ 10
0
votes
1
reply
1.6k
views
Trouble with importing transcript counts with Salmon
Salmon tximport RNAseq EdgeR
updated 3.2 years ago by ★ 5.0k • written 3.2 years ago by • 0
1
vote
2
replies
1.4k
views
error loading kallisto output in tximport
file.exists false kallisto tximport
3.2 years ago cta • 0
2
votes
3
replies
2.7k
views
How to convert transcript counts to gene counts in R?
DESeq2 tximport
updated 9 months ago by • 0 • written 3.3 years ago by ▴ 50
3
votes
3
replies
1.8k
views
What is the correct way to import transcript abundances from 3' Quantseq results that calculated by kallisto?
tximport tximportData Quantseq kallisto
3.3 years ago • updated 3.2 years ago duhwa.lee • 0
1
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2
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2.7k
views
transcripts missing from tx2gene
tximport
3.4 years ago • updated 3.3 years ago Erick • 0
0
votes
1
reply
1.1k
views
tximport: not all(file.exists(files)) are true
tximport
updated 3.4 years ago by 43k • written 3.4 years ago by • 0
3
votes
1
reply
4.4k
views
Understanding tximport working with salmon outputs
Transcriptomics tximport
updated 3.4 years ago by ★ 5.0k • written 3.4 years ago by ▴ 10
297 results • Page 1 of 6
Recent ...
Replies
Answer: lfc shrinkage estimator in DESeq2 by plumsgorillas • 0
You are on the right track. In DESeq2, raw log2 fold changes are often noisy and can be misleading, especially for genes with low counts. A…
Answer: Array weights in dpcDE by Gordon Smyth 53k
The uncertainty of quantification is fully accounted for in the dpcDE() analysis, including in the computation of sample weights. However,…
Answer: lfc shrinkage estimator in DESeq2 by Michael Love 43k
Try the vignette which has a lot of information on these type of questions.
Comment: limpa analysis advice by Gordon Smyth 53k
The DPC slope is beta1. The estimated slopes for your data look pretty low, lower than I've ever used for a real dataset. Nevertheless, as …
Comment: limpa analysis advice by SamGG ▴ 360
Thanks for your feedback and for reassuring me. :-) As you suggested, I tried dpcCN() and set the slope to 0.7 in addition to the standard…
Votes
A: DESeq2: Is it possible to convert read counts to expression values via TPM and r
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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