Showing : tximport • reset
0
votes
3
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208
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Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport DESeq2
updated 22 days ago by ★ 3.4k • written 24 days ago by • 0
0
votes
4
replies
269
views
Handle zero effective gene length when tximport RSEM results
tximport edgeR
updated 23 days ago by 40k • written 4 weeks ago by • 0
2
votes
3
replies
310
views
Import Salmon data with tximport and pool technical replicates
tximport edgeR
written 5 weeks ago by • 0
1
vote
2
replies
216
views
IsoformSwitchAnalyzeR: What are the SV values created in design matrix?
salmon IsoformSwitchAnalyzeR tximport RNASeqData
updated 7 weeks ago by ▴ 120 • written 8 weeks ago by ▴ 10
2
votes
9
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595
views
Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport tximportData DESeq2
11 weeks ago • updated 10 weeks ago Ndimensional ▴ 20
0
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2
replies
288
views
tximport error in reading salmon output files?
tximport tximportData
3 months ago barrypraveen • 0
0
votes
1
reply
293
views
Which file in tximport should I use for DESeq2 analysis?
tximport DESeq2
updated 4 months ago by 63k • written 4 months ago by • 0
2
votes
1
reply
300
views
scaledTPM for DESeq2 using tximport
DESeq2 tximport
updated 4 months ago by 40k • written 4 months ago by • 0
3
votes
7
replies
551
views
failed to use tximport for creating count matrix from kallisto
tximport kallisto
4 months ago Yijing • 0
0
votes
2
replies
355
views
Error in H5Fopen
rhdf5 Rhdf5lib kallisto tximport
4 months ago Yijing • 0
1
vote
3
replies
397
views
tximport error
tximport r
updated 5 months ago by 40k • written 5 months ago by • 0
0
votes
2
replies
414
views
combining multiple salmon runs after tximport
tximport RNASeq salmon
updated 7 months ago by ★ 3.4k • written 7 months ago by • 0
1
vote
5
replies
631
views
tximport: kallisto + GENCODE transcript sanitization
tximport
updated 7 months ago by 40k • written 7 months ago by ▴ 90
3
votes
5
replies
750
views
Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
7 months ago mohammedtoufiq91 ▴ 10
0
votes
1
reply
389
views
Is it possible to convert transcript-level to gene-level dataset to use it in DESeq2 ?
DESeq2 Transcriptomics tximport deseq txi
updated 8 months ago by ★ 1.5k • written 8 months ago by ▴ 10
0
votes
2
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478
views
how to match salmon output to txname
GenomicFeatures tximport salmon
written 8 months ago by • 0
0
votes
1
reply
382
views
Missing transcript
DESeq2 tximport salmon
updated 8 months ago by ★ 3.4k • written 8 months ago by • 0
2
votes
1
reply
389
views
Confused about tximport-DESeq2 setup
DESeq2 tximport salmon
updated 8 months ago by ★ 3.4k • written 8 months ago by • 0
2
votes
2
replies
630
views
Normalizing Salmon output count data matrix using DESeq2
DESeq2 tximport counts Salmon
written 8 months ago by • 0
0
votes
2
replies
461
views
Differentially expression analysis of orthologous genes between two species
DESeq2 tximport
9 months ago Konstantinos • 0
2
votes
3
replies
744
views
Error while reading rsem files in tximport
DESeq2 tximport rsem RNASeq tximportData
9 months ago mohammedtoufiq91 ▴ 10
4
votes
3
replies
603
views
tx2gene object trouble when working with kallisto and A.thaliana
tx2gene tximport Arabidopsis_thaliana kallisto
updated 10 months ago by 63k • written 10 months ago by ▴ 10
0
votes
1
reply
535
views
Trouble with importing transcript counts with Salmon
Salmon tximport RNAseq EdgeR
updated 10 months ago by ★ 3.4k • written 10 months ago by • 0
1
vote
2
replies
474
views
error loading kallisto output in tximport
file.exists false kallisto tximport
10 months ago cta • 0
2
votes
2
replies
746
views
How to convert transcript counts to gene counts in R?
DESeq2 tximport
11 months ago L ▴ 50
3
votes
3
replies
547
views
What is the correct way to import transcript abundances from 3' Quantseq results that calculated by kallisto?
tximport tximportData Quantseq kallisto
11 months ago • updated 10 months ago duhwa.lee • 0
1
vote
2
replies
856
views
transcripts missing from tx2gene
tximport
12 months ago Erick • 0
0
votes
1
reply
417
views
tximport: not all(file.exists(files)) are true
tximport
updated 12 months ago by 40k • written 12 months ago by • 0
2
votes
1
reply
847
views
Understanding tximport working with salmon outputs
Transcriptomics tximport
updated 12 months ago by ★ 3.4k • written 12 months ago by ▴ 10
3
votes
4
replies
656
views
difference between txi$counts and txi$abundance when countsFromAbundance is true
RNAseq tximport
updated 12 months ago by ★ 3.4k • written 12 months ago by • 0
0
votes
3
replies
586
views
tximport error
error tximport
updated 12 months ago by 40k • written 12 months ago by • 0
5
votes
6
replies
929
views
Selecting individual samples from tximport and DGE matrix design with missing biological replicate
DESeq2 limma tximport
updated 12 months ago by 48k • written 12 months ago by • 0
0
votes
4
replies
730
views
Alternative for wininet method in tximeta
DESeq2 tximport tximportData tximeta
14 months ago uhlkatie • 0
2
votes
8
replies
1.1k
views
RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM tximport scRNAseq DESeq2
15 months ago • updated 14 months ago Kelen ▴ 10
1
vote
3
replies
1.1k
views
miRNA differential expression analysis - treat as transcript level?
tximport DESeq2 edgeR swish miRNA
updated 15 months ago by 40k • written 15 months ago by • 0
0
votes
1
reply
642
views
Function Request for Rsubread or tximport: parsing command-line featureCounts output
tximport Rsubread
updated 16 months ago by ★ 3.4k • written 16 months ago by ▴ 10
0
votes
1
reply
593
views
Why TxImport Abundance is slightly different from manually added TPMs?
tximport R
updated 16 months ago by 40k • written 16 months ago by • 0
2
votes
3
replies
811
views
Problem with tximport IDs
tximport tx2gene rnas DESeq2 RNASeqData
16 months ago Maka • 0
5
votes
4
replies
1.5k
views
confused with tximport counts abundance using salmon input
RNASeq tximport
17 months ago Al90 ▴ 10
0
votes
2
replies
1.8k
views
tximport ERROR : all(file.exists(files)) is not TRUE
Linux R tximport
19 months ago nakane_clan • 0
2
votes
5
replies
1.3k
views
from kallisto to deseq2 analysis
biomaRt DESeq2 tximport
19 months ago Marianna ▴ 10
2
votes
3
replies
716
views
Import RSEM output without sample data
DESeq2 tximportData tximport
updated 19 months ago by 40k • written 19 months ago by • 0
0
votes
1
reply
536
views
tximport
salmon tximport
updated 19 months ago by 40k • written 19 months ago by • 0
0
votes
1
reply
642
views
Ensembl dataset version
tximport rna rnaseqGene biomaRt
updated 20 months ago by ★ 3.4k • written 20 months ago by • 0
0
votes
3
replies
997
views
tximport question on what counts to use for LogFC calculations
tximport
updated 22 months ago by 40k • written 22 months ago by • 0
0
votes
4
replies
1.2k
views
Filtering output from tximport
tximport Salmon
updated 22 months ago by 40k • written 22 months ago by • 0
1
vote
5
replies
2.2k
views
tximport error: all(txId == raw[[txIdCol]]) is not TRUE
tximport
updated 9 weeks ago by 40k • written 22 months ago by • 0
2
votes
1
reply
1.2k
views
How to normalize Kallisto count matrix collapsed at gene-level with TMM/DESeq2?
DESeq2 tximport Kallisto TMM edgeR
updated 23 months ago by 40k • written 23 months ago by • 0
0
votes
1
reply
946
views
tximport samples with separate tx2gene maps
tximport
updated 22 months ago by 40k • written 23 months ago by • 0
0
votes
2
replies
1.0k
views
Error message when importing my quant.sf files into R using tximport; should I set 'ignoreTxVersion' to True or False?
Salmon ignoreTxVersion tximport
updated 2.1 years ago by 40k • written 2.1 years ago by • 0
50 results • Page 1 of 1
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Comment: List of Deprecated Packages for Bioc3.18 by Hervé Pagès 16k
Also the source package is not available [in BioC 3.17](https://bioconductor.org/packages/3.17/CancerInSilico) which means that the package…
Answer: DelayedArray::read_sparse_block by Hervé Pagès 16k
Hi Koki, Sorry again for the slow response. `read_sparse_block()` has been around for years. It's a generic function defined in the *…
Comment: Speeding up of DelayedArray::write_block() by Hervé Pagès 16k
Sorry for missing that one too. When writting blocks to an HDF5 file, the `write_block()` method for HDF5RealizationSink or TENxRealizatio…
Comment: Speeding up of DelayedArray::write_block() by Hervé Pagès 16k
Hi Koki, sorry for not seeing this before. > will SparseArraySeed in DelayedArray be replaced by this new sparse array format? Yes it wil…
Comment: Manual creation of qPCRset does not work by Ed Siefker ▴ 230
Thanks! This works for me.
Votes
Comment: List of Deprecated Packages for Bioc3.18
Answer: Manual creation of qPCRset does not work
Answer: MDS plot edgeR
A: legend with gradient in ComplexHeatmap
Comment: comparing contrasts in edger/lima using makeContrasts function
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