Showing : txImport • reset
0
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4
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153
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Alternative for wininet method in tximeta
DESeq2 tximport tximportData tximeta
6 weeks ago uhlkatie • 0
1
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3
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338
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miRNA differential expression analysis - treat as transcript level?
tximport DESeq2 edgeR swish miRNA
updated 7 weeks ago by 37k • written 8 weeks ago by • 0
2
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8
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341
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RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM tximport scRNAseq DESeq2
7 weeks ago • updated 6 weeks ago Kelen • 0
0
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1
reply
164
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Function Request for Rsubread or tximport: parsing command-line featureCounts output
tximport Rsubread
updated 12 weeks ago by ★ 1.4k • written 12 weeks ago by ▴ 10
0
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1
reply
155
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Why TxImport Abundance is slightly different from manually added TPMs?
tximport R
updated 3 months ago by 37k • written 3 months ago by • 0
2
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3
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265
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Problem with tximport IDs
tximport tx2gene rnas DESeq2 RNASeqData
3 months ago Maka • 0
2
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4
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272
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confused with tximport counts abundance using salmon input
RNASeq tximport
4 months ago Al90 • 0
0
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2
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409
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tximport ERROR : all(file.exists(files)) is not TRUE
Linux R tximport
5 months ago nakane_clan • 0
2
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5
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412
views
from kallisto to deseq2 analysis
biomaRt DESeq2 tximport
6 months ago Marianna • 0
2
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3
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298
views
Import RSEM output without sample data
DESeq2 tximportData tximport
updated 6 months ago by 37k • written 6 months ago by • 0
0
votes
1
reply
205
views
tximport
salmon tximport
updated 6 months ago by 37k • written 6 months ago by • 0
0
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1
reply
248
views
Ensembl dataset version
tximport rna rnaseqGene biomaRt
updated 7 months ago by ★ 1.4k • written 7 months ago by • 0
0
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3
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473
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tximport question on what counts to use for LogFC calculations
tximport
updated 8 months ago by 37k • written 8 months ago by • 0
0
votes
4
replies
578
views
Filtering output from tximport
tximport Salmon
updated 9 months ago by 37k • written 9 months ago by • 0
0
votes
1
reply
508
views
tximport samples with separate tx2gene maps
tximport
updated 9 months ago by 37k • written 10 months ago by • 0
1
vote
3
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750
views
tximport error: all(txId == raw[[txIdCol]]) is not TRUE
tximport
9 months ago nicolette.sipperly • 0
2
votes
1
reply
364
views
How to normalize Kallisto count matrix collapsed at gene-level with TMM/DESeq2?
DESeq2 tximport Kallisto TMM edgeR
updated 10 months ago by 37k • written 10 months ago by • 0
0
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2
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475
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 11 months ago by 37k • written 12 months ago by • 0
1
vote
2
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374
views
tximeta countsFromAbundance for downstream analysis
tximeta tximport
12 months ago paulimer • 0
2
votes
3
replies
473
views
importing RSEM isoform to Gene Name with tximport
tximport
updated 13 months ago by 60k • written 13 months ago by ▴ 10
2
votes
2
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382
views
Issues with Tximport
tximport
14 months ago bryce.thomas • 0
0
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3
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727
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Tximport error message - colnames
tximport
updated 14 months ago by 37k • written 14 months ago by • 0
0
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5
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562
views
Tximport/DESeq2 Normalization Process
tximport Normalization DESeq2
updated 14 months ago by 37k • written 14 months ago by • 0
4
votes
3
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551
views
Concatenating expression counts from different RNA-seq quantification tools
tximport HERVs edgeR DESeq2
updated 14 months ago by 37k • written 14 months ago by ▴ 30
0
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1
reply
392
views
Multi-factor Analysis in DeSEQ2
tximport R tximportData RNASeq DESeq2
updated 15 months ago by 37k • written 15 months ago by • 0
0
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6
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557
views
Problem with Tximport to DESeq2
TxDb.Mmusculus.UCSC.mm10.ensGene DESeq2 tximport
15 months ago zli1 • 0
2
votes
2
replies
425
views
TxImport when quant.sf files have different index files
tximport DESeq2
17 months ago mprnl • 0
0
votes
1
reply
415
views
tximport rowsum error
tximport
17 months ago Ezgi ▴ 30
0
votes
1
reply
582
views
DESeq2, tximport normalization, normalization factors, size factors
tximport DESeq2 normalizationfactors sizefactors
updated 17 months ago by 37k • written 17 months ago by • 0
0
votes
2
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393
views
Pair-wise DESeq2 using tximport (running time and multi-threading)
tximport DESeq2
updated 17 months ago by 37k • written 17 months ago by • 0
1
vote
2
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724
views
Regarding transcripts to gene ID conversion in tximport
salmon tximport DESeq2
17 months ago Nikolay Ivanov • 0
1
vote
2
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1.4k
views
Importing data into the DESeq2 pipeline using tximport
DESeq2 tximport
18 months ago Nikolay Ivanov • 0
0
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2
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391
views
tximport no counts from abundance using EnsDb.Hsapiens.v86
salmon EnsDb.Hsapiens.v86 tximport
updated 18 months ago by 60k • written 18 months ago by • 0
0
votes
7
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779
views
Problem with Tximport
tximportData tximport
18 months ago agoesmartini • 0
0
votes
1
reply
379
views
tximport error importing expected counts file from RSEM
RSEM tximport
updated 19 months ago by 37k • written 19 months ago by • 0
2
votes
1
reply
790
views
DESeq usage of transcript TPM after tximport
tximport
updated 20 months ago by 37k • written 20 months ago by • 0
2
votes
1
reply
466
views
tximport with salmon bootstraps and edger/deseq2
tximport
updated 20 months ago by 37k • written 20 months ago by • 0
0
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5
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505
views
sumarizeToGene is dropping transcripts, how to debug
sumarizeToGene tximport
updated 19 months ago by 37k • written 20 months ago by ▴ 20
6
votes
6
replies
1.1k
views
Transformation of raw RSEM gene expression estimates with variance stabilizing transformation and tximport R package
DESeq2 VST rsem tximport
20 months ago svlachavas ▴ 800
0
votes
1
reply
433
views
How to use tx import on output of abundance file
tximportData tximport
updated 21 months ago by 3.6k • written 21 months ago by • 0
1
vote
4
replies
504
views
tximport abundanceCol parameter not functioning for rsem data
tximport rsem transcript abundance TPM FPKM
updated 21 months ago by 37k • written 23 months ago by • 0
0
votes
1
reply
599
views
importing RSEM data into DESeq2
deseq2 tximport
updated 22 months ago by 37k • written 22 months ago by ▴ 10
1
vote
9
replies
665
views
Question: Error running summarizeToGene() - RNA Seq Bioconductor pipeline
tximeta tximport deseq2
updated 23 months ago by 37k • written 23 months ago by ▴ 20
0
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8
replies
702
views
Importing RSEM with tximport
tximport RSEM import error
updated 23 months ago by 37k • written 24 months ago by ▴ 50
2
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8
replies
1.8k
views
Which R version is needed for tximport package?
tximport package R version install tximport
24 months ago harelarik ▴ 50
0
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5
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679
views
Error using DRIMSeq with Salmon count data
DRIMSeq tximport txdb Salmon
updated 2.0 years ago by 37k • written 2.0 years ago by • 0
2
votes
2
replies
450
views
RSEM for DESeq2 without abundance matrix
tximport deseq2 rsem
updated 2.0 years ago by 37k • written 2.0 years ago by ▴ 20
1
vote
1
reply
305
views
Error in importing Salmon quantifications into R with tximport
deseq2 tximport
updated 2.0 years ago by 37k • written 2.0 years ago by ▴ 10
1
vote
2
replies
370
views
How tximport calculate abundance
tximport abundance
updated 2.0 years ago by 37k • written 2.0 years ago by • 0
2
votes
1
reply
544
views
tximport samples.txt file mandatory vs. optional colnames?
tximport salmon deseq2
updated 2.0 years ago by 37k • written 2.0 years ago by ▴ 20
50 results • Page 1 of 1
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Comment: How to retrieve Entrez IDs using Gene Symbols? by Basti ▴ 390
Cross-posted : https://www.biostars.org/p/9535046/#9535054
Comment: An ESR essay about software design, and how it applies to Bioconductor by Gary • 0
It's relevant for me, thank you for the information!
Comment: An ESR essay about software design, and how it applies to Bioconductor by Gary • 0
Thank you for sharing!
Comment: conditional command within GRanges by Basti ▴ 390
I can't reproduce your issue because you did not provided an example of your dataset (example with `dput(head(data1))`, but in the first ca…
Comment: Error in Create switchAnalyzeRlist by k.vitting.seerup ▴ 120
That sounds like you have the wrong version of the annotation compared to which version you used for the quantification?
Votes
Answer: WHat is the difference between DEG and TopVarGenes in DESEq2?
Answer: WHat is the difference between DEG and TopVarGenes in DESEq2?
A: EGSEA error during report generation: "only 0's may be mixed with negative subsc
Answer: mapToAlignments_issue
Analysis of peaks generated from Homer using Diffbind
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