Showing : TXIMPORT • reset
0
votes
1
reply
461
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discrepancy in IDs from file and tx2gene (IDs don't match)
tximport DESeq2
updated 3 months ago by 68k • written 3 months ago by • 0
0
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1
reply
658
views
Which GTF file to use for creation of tx2gene files?
tximport
updated 4 months ago by 43k • written 4 months ago by • 0
0
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3
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914
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Many transcripts missing from tx2gene created from Ensembl GTF file
kallisto tximport ensembl
updated 4 months ago by • 0 • written 4 months ago by • 0
0
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1
reply
434
views
Best tximport quant.genes.sf
tximport tximeta Bioconductor
updated 5 months ago by ★ 5.0k • written 5 months ago by • 0
0
votes
4
replies
1.4k
views
Error in H5Dclose(h5dataset) when trying to read in kallisto h5 files
tximport rhdf5
7 months ago • updated 6 months ago Sofia • 0
0
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4
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814
views
Using tximport for kallisto aligned TOIL data
kallisto tximport TOIL
7 months ago Nicholas • 0
0
votes
11
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1.4k
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Problems with oarfish + tximport + swish
fishpond tximport tximeta
updated 9 months ago by • 0 • written 9 months ago by • 0
1
vote
2
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1.1k
views
Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport DESeq2 GSVA
10 months ago georgii.vdovin • 0
4
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5
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1.3k
views
DESeq Input from Salmon + tximport/tximeta
tximportData summarizeToGene tximport DESeq2 salmon
11 months ago LuciaNhu • 0
0
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2
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695
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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 12 months ago by 43k • written 12 months ago by • 0
0
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2
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664
views
tximport data import
tximport
updated 13 months ago by 43k • written 13 months ago by • 0
1
vote
2
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1.3k
views
How to use specific size factors and average transcript lengths from tximport in DESeq2?
DESeq2 tximport
14 months ago grothmn • 0
1
vote
2
replies
2.7k
views
using tximport with STAR transcript-quantification output
tximport deseq2 STAR
updated 16 months ago by ▴ 40 • written 6.0 years ago by • 0
0
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4
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921
views
Create count matrix from multible quant sf files from different directories
tximportData tximport salmon
16 months ago JG13 • 0
0
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2
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897
views
edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
19 months ago Marianna ▴ 20
0
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2
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980
views
Clarification on Library Size Normalization After Using tximport with countsFromAbundance="lengthScaledTPM"
tximport
updated 19 months ago by 43k • written 19 months ago by • 0
2
votes
1
reply
782
views
Creating data matrix in Deseq2 from tximport data invalid class SummarizedExperiment object
DESeq2 tximport
updated 19 months ago by ★ 5.0k • written 19 months ago by • 0
2
votes
3
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3.5k
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR tximport RNASeq DESeq2
updated 22 months ago by ★ 1.4k • written 22 months ago by • 0
0
votes
1
reply
1.0k
views
tximport error with rsem files
rsem tximport
updated 22 months ago by ★ 5.0k • written 22 months ago by • 0
3
votes
2
replies
1.3k
views
tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
tximport DESeq2
updated 23 months ago by 68k • written 23 months ago by • 0
0
votes
3
replies
1.2k
views
Tximport Error - transcripts in quant files are not the same as tx2gene
salmon tximport deseq2
updated 2.0 years ago by 43k • written 2.0 years ago by • 0
10
votes
11
replies
3.5k
views
tximport error: vroom
tximport
updated 2.0 years ago by • 0 • written 2.1 years ago by ▴ 40
2
votes
3
replies
1.5k
views
Import Salmon data with tximport and pool technical replicates
tximport edgeR
written 2.2 years ago by • 0
5
votes
13
replies
4.2k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport DESeq2
updated 2.1 years ago by 43k • written 2.2 years ago by • 0
2
votes
4
replies
2.0k
views
Handle zero effective gene length when tximport RSEM results
tximport edgeR
updated 2.2 years ago by 43k • written 2.2 years ago by ▴ 10
1
vote
2
replies
2.7k
views
IsoformSwitchAnalyzeR: What are the SV values created in design matrix?
salmon IsoformSwitchAnalyzeR tximport RNASeqData
updated 2.2 years ago by ▴ 120 • written 2.2 years ago by ▴ 10
2
votes
9
replies
2.3k
views
Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport tximportData DESeq2
2.3 years ago Ndimensional ▴ 20
0
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2
replies
1.2k
views
tximport error in reading salmon output files?
tximport tximportData
updated 21 months ago by • 0 • written 2.4 years ago by • 0
0
votes
1
reply
1.2k
views
Which file in tximport should I use for DESeq2 analysis?
tximport DESeq2
updated 2.4 years ago by 68k • written 2.4 years ago by • 0
2
votes
1
reply
1.4k
views
scaledTPM for DESeq2 using tximport
DESeq2 tximport
updated 2.5 years ago by 43k • written 2.5 years ago by • 0
3
votes
7
replies
2.0k
views
failed to use tximport for creating count matrix from kallisto
tximport kallisto
2.5 years ago Yijing • 0
0
votes
2
replies
1.6k
views
Error in H5Fopen
rhdf5 Rhdf5lib kallisto tximport
2.5 years ago Yijing • 0
1
vote
3
replies
1.6k
views
tximport error
tximport r
updated 2.5 years ago by 43k • written 2.5 years ago by • 0
0
votes
2
replies
1.7k
views
combining multiple salmon runs after tximport
tximport RNASeq salmon
updated 2.7 years ago by ★ 5.0k • written 2.7 years ago by • 0
1
vote
5
replies
2.0k
views
tximport: kallisto + GENCODE transcript sanitization
tximport
updated 2.7 years ago by 43k • written 2.7 years ago by ▴ 90
6
votes
10
replies
4.0k
views
Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
updated 18 months ago by • 0 • written 2.7 years ago by ▴ 10
0
votes
1
reply
1.2k
views
Is it possible to convert transcript-level to gene-level dataset to use it in DESeq2 ?
DESeq2 Transcriptomics tximport deseq txi
updated 2.8 years ago by ★ 1.6k • written 2.8 years ago by ▴ 10
0
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2
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1.5k
views
how to match salmon output to txname
GenomicFeatures tximport salmon
written 2.8 years ago by • 0
0
votes
1
reply
1.4k
views
Missing transcript
DESeq2 tximport salmon
updated 2.8 years ago by ★ 5.0k • written 2.8 years ago by • 0
2
votes
5
replies
2.6k
views
Normalizing Salmon output count data matrix using DESeq2
DESeq2 tximport counts Salmon
updated 20 months ago by 43k • written 2.8 years ago by • 0
0
votes
2
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1.4k
views
Differentially expression analysis of orthologous genes between two species
DESeq2 tximport
2.9 years ago Konstantinos • 0
2
votes
3
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2.1k
views
Error while reading rsem files in tximport
DESeq2 tximport rsem RNASeq tximportData
2.9 years ago mohammedtoufiq91 ▴ 10
4
votes
3
replies
1.9k
views
tx2gene object trouble when working with kallisto and A.thaliana
tx2gene tximport Arabidopsis_thaliana kallisto
updated 2.9 years ago by 68k • written 2.9 years ago by ▴ 10
0
votes
1
reply
1.5k
views
Trouble with importing transcript counts with Salmon
Salmon tximport RNAseq EdgeR
updated 2.9 years ago by ★ 5.0k • written 2.9 years ago by • 0
1
vote
2
replies
1.4k
views
error loading kallisto output in tximport
file.exists false kallisto tximport
3.0 years ago cta • 0
2
votes
3
replies
2.6k
views
How to convert transcript counts to gene counts in R?
DESeq2 tximport
updated 6 months ago by • 0 • written 3.0 years ago by ▴ 50
3
votes
3
replies
1.7k
views
What is the correct way to import transcript abundances from 3' Quantseq results that calculated by kallisto?
tximport tximportData Quantseq kallisto
3.0 years ago duhwa.lee • 0
1
vote
2
replies
2.5k
views
transcripts missing from tx2gene
tximport
3.1 years ago Erick • 0
0
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1
reply
1.1k
views
tximport: not all(file.exists(files)) are true
tximport
updated 3.1 years ago by 43k • written 3.1 years ago by • 0
3
votes
1
reply
3.8k
views
Understanding tximport working with salmon outputs
Transcriptomics tximport
updated 3.1 years ago by ★ 5.0k • written 3.1 years ago by ▴ 10
297 results • Page 1 of 6
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Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Aaron already answered your question. If you have an HDF5 file, it will be read in as a `TENxMatrix` object, which isn't actually read in -…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0
Very strange. We have the same package versions. I tried adding the mtx.class, type, and delayed arguments, but it's still making the coun…
Comment: DESeq2 for candidate gene analysis by piffelpaff ▴ 20
thank you so much for answering Dr. Love!
Answer: DESeq2 for candidate gene analysis by Michael Love 43k
Your plan 1 is reasonable. Run DESeq2 on the whole dataset to obtain size factors and moderated dispersion estimates and then extract the u…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Oh. ``` > z <- read10xCounts(c(tmpdir, tmpdir), mtx.class = "SVT_SparseMatrix", delayed = TRUE) > class(counts(z)) [1] "DelayedMatrix" att…
Votes
A: Multi-level experiments in Limma
Answer: Should voomWithQualityWeights still be used when the sample-specific weights var
Answer: DESeq2 for candidate gene analysis
DESeq2 for candidate gene analysis
Answer: DESeq2 for candidate gene analysis
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