Showing : Tximport • reset
0
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2
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36
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Problems with oarfish + tximport + swish
fishpond tximport tximeta
updated 2 hours ago by 43k • written 5 hours ago by • 0
1
vote
2
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470
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Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport DESeq2 GSVA
5 weeks ago • updated 4 weeks ago georgii.vdovin • 0
4
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5
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674
views
DESeq Input from Salmon + tximport/tximeta
tximportData summarizeToGene tximport DESeq2 salmon
10 weeks ago LuciaNhu • 0
0
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2
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411
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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 3 months ago by 43k • written 3 months ago by • 0
0
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2
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441
views
tximport data import
tximport
updated 4 months ago by 43k • written 4 months ago by • 0
1
vote
2
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821
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How to use specific size factors and average transcript lengths from tximport in DESeq2?
DESeq2 tximport
5 months ago grothmn • 0
1
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2
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2.3k
views
using tximport with STAR transcript-quantification output
tximport deseq2 STAR
updated 7 months ago by ▴ 40 • written 5.2 years ago by • 0
0
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4
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627
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Create count matrix from multible quant sf files from different directories
tximportData tximport salmon
7 months ago JG13 • 0
0
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2
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579
views
edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
9 months ago Marianna ▴ 20
0
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2
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616
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Clarification on Library Size Normalization After Using tximport with countsFromAbundance="lengthScaledTPM"
tximport
updated 9 months ago by 43k • written 9 months ago by • 0
2
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1
reply
528
views
Creating data matrix in Deseq2 from tximport data invalid class SummarizedExperiment object
DESeq2 tximport
updated 10 months ago by ★ 4.6k • written 10 months ago by • 0
2
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3
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2.5k
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR tximport RNASeq DESeq2
updated 13 months ago by ★ 1.4k • written 13 months ago by • 0
0
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1
reply
738
views
tximport error with rsem files
rsem tximport
updated 13 months ago by ★ 4.6k • written 13 months ago by • 0
3
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2
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1.0k
views
tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
tximport DESeq2
updated 13 months ago by 67k • written 13 months ago by • 0
0
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3
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837
views
Tximport Error - transcripts in quant files are not the same as tx2gene
salmon tximport deseq2
updated 15 months ago by 43k • written 15 months ago by • 0
10
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11
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2.8k
views
tximport error: vroom
tximport
updated 14 months ago by • 0 • written 15 months ago by ▴ 40
2
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3
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1.2k
views
Import Salmon data with tximport and pool technical replicates
tximport edgeR
written 17 months ago by • 0
4
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13
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2.8k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport DESeq2
updated 15 months ago by 43k • written 16 months ago by • 0
0
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4
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1.5k
views
Handle zero effective gene length when tximport RSEM results
tximport edgeR
updated 16 months ago by 43k • written 17 months ago by • 0
1
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2
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2.3k
views
IsoformSwitchAnalyzeR: What are the SV values created in design matrix?
salmon IsoformSwitchAnalyzeR tximport RNASeqData
updated 17 months ago by ▴ 120 • written 17 months ago by ▴ 10
2
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9
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1.8k
views
Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport tximportData DESeq2
18 months ago Ndimensional ▴ 20
0
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2
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949
views
tximport error in reading salmon output files?
tximport tximportData
updated 11 months ago by • 0 • written 19 months ago by • 0
0
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1
reply
922
views
Which file in tximport should I use for DESeq2 analysis?
tximport DESeq2
updated 20 months ago by 67k • written 20 months ago by • 0
2
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1
reply
1.1k
views
scaledTPM for DESeq2 using tximport
DESeq2 tximport
updated 20 months ago by 43k • written 20 months ago by • 0
3
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7
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1.6k
views
failed to use tximport for creating count matrix from kallisto
tximport kallisto
20 months ago Yijing • 0
0
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2
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1.3k
views
Error in H5Fopen
rhdf5 Rhdf5lib kallisto tximport
20 months ago Yijing • 0
1
vote
3
replies
1.3k
views
tximport error
tximport r
updated 21 months ago by 43k • written 21 months ago by • 0
0
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2
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1.3k
views
combining multiple salmon runs after tximport
tximport RNASeq salmon
updated 23 months ago by ★ 4.6k • written 23 months ago by • 0
1
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5
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1.7k
views
tximport: kallisto + GENCODE transcript sanitization
tximport
updated 23 months ago by 43k • written 23 months ago by ▴ 90
6
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10
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2.8k
views
Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
updated 9 months ago by • 0 • written 23 months ago by ▴ 10
0
votes
1
reply
983
views
Is it possible to convert transcript-level to gene-level dataset to use it in DESeq2 ?
DESeq2 Transcriptomics tximport deseq txi
updated 24 months ago by ★ 1.5k • written 2.0 years ago by ▴ 10
0
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2
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1.2k
views
how to match salmon output to txname
GenomicFeatures tximport salmon
written 2.0 years ago by • 0
0
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1
reply
1.1k
views
Missing transcript
DESeq2 tximport salmon
updated 2.0 years ago by ★ 4.6k • written 2.0 years ago by • 0
2
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1
reply
1.0k
views
Confused about tximport-DESeq2 setup
DESeq2 tximport salmon
updated 2.0 years ago by ★ 4.6k • written 2.0 years ago by • 0
2
votes
5
replies
2.0k
views
Normalizing Salmon output count data matrix using DESeq2
DESeq2 tximport counts Salmon
updated 10 months ago by 43k • written 2.1 years ago by • 0
0
votes
2
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1.1k
views
Differentially expression analysis of orthologous genes between two species
DESeq2 tximport
2.1 years ago Konstantinos • 0
2
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3
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1.7k
views
Error while reading rsem files in tximport
DESeq2 tximport rsem RNASeq tximportData
2.1 years ago mohammedtoufiq91 ▴ 10
4
votes
3
replies
1.5k
views
tx2gene object trouble when working with kallisto and A.thaliana
tx2gene tximport Arabidopsis_thaliana kallisto
updated 2.1 years ago by 67k • written 2.2 years ago by ▴ 10
0
votes
1
reply
1.2k
views
Trouble with importing transcript counts with Salmon
Salmon tximport RNAseq EdgeR
updated 2.2 years ago by ★ 4.6k • written 2.2 years ago by • 0
1
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2
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1.1k
views
error loading kallisto output in tximport
file.exists false kallisto tximport
2.2 years ago cta • 0
2
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3
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1.8k
views
How to convert transcript counts to gene counts in R?
DESeq2 tximport
written 2.2 years ago by ▴ 50
3
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3
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1.4k
views
What is the correct way to import transcript abundances from 3' Quantseq results that calculated by kallisto?
tximport tximportData Quantseq kallisto
2.2 years ago duhwa.lee • 0
1
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2
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2.1k
views
transcripts missing from tx2gene
tximport
2.3 years ago Erick • 0
0
votes
1
reply
907
views
tximport: not all(file.exists(files)) are true
tximport
updated 2.3 years ago by 43k • written 2.3 years ago by • 0
3
votes
1
reply
2.7k
views
Understanding tximport working with salmon outputs
Transcriptomics tximport
updated 2.3 years ago by ★ 4.6k • written 2.3 years ago by ▴ 10
3
votes
4
replies
1.9k
views
difference between txi$counts and txi$abundance when countsFromAbundance is true
RNAseq tximport
updated 2.3 years ago by ★ 4.6k • written 2.3 years ago by • 0
0
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3
replies
1.3k
views
tximport error
error tximport
updated 2.3 years ago by 43k • written 2.4 years ago by • 0
5
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6
replies
2.0k
views
Selecting individual samples from tximport and DGE matrix design with missing biological replicate
DESeq2 limma tximport
updated 2.3 years ago by 52k • written 2.4 years ago by • 0
0
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4
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1.5k
views
Alternative for wininet method in tximeta
DESeq2 tximport tximportData tximeta
2.5 years ago uhlkatie • 0
1
vote
3
replies
2.3k
views
miRNA differential expression analysis - treat as transcript level?
tximport DESeq2 edgeR swish miRNA
updated 2.6 years ago by 43k • written 2.6 years ago by • 0
50 results • Page 1 of 1
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Replies
Comment: Why did PCA plots look exactly the same after adjusting for batch covariate in D by Michael Love 43k
hi, for questions about what statistical analysis approach to use, I recommend you work with a local statistician or someone familiar with …
Comment: Problems with oarfish + tximport + swish by Michael Love 43k
I'm not certain that this will work with Oarfish, the documentation only mentions Salmon and piscem. I'd use tximport for now.
Answer: Problems with oarfish + tximport + swish by Michael Love 43k
> This is fine Did tximeta() print that a matching transcriptome was found?
Answer: DESeq2 Heatmap by swbarnes2 ★ 1.4k
> However, I've been asked why the first column (vehicle/control) isn't > entirely zero on the log fold change (logFC) expression scale. …
Comment: Biomart and ensembl not working? by James W. MacDonald 67k
``` > library(biomaRt) > mart <- useEnsembl("ensembl","hsapiens_gene_ensembl") Ensembl site unresponsive, trying useast mirror > mart Objec…
Votes
Answer: Limma Interaction Effect with Covariates
Comment: DESeq2 for single cell pseudobulk processing
C: Limma: how to get same output as topTable but for all the genes ?
A: Processing agilent data by limma
A: Linear regression in DESeq2
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