Showing : txImport • reset
1
vote
7
replies
205
views
RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM tximport scRNAseq DESeq2
updated 2 days ago by 37k • written 10 days ago by • 0
0
votes
4
replies
75
views
Alternative for wininet method in tximeta
DESeq2 tximport tximportData tximeta
3 days ago uhlkatie • 0
1
vote
3
replies
252
views
miRNA differential expression analysis - treat as transcript level?
tximport DESeq2 edgeR swish miRNA
updated 7 days ago by 37k • written 13 days ago by • 0
0
votes
1
reply
132
views
Function Request for Rsubread or tximport: parsing command-line featureCounts output
tximport Rsubread
updated 6 weeks ago by ★ 1.3k • written 6 weeks ago by ▴ 10
0
votes
1
reply
118
views
Why TxImport Abundance is slightly different from manually added TPMs?
tximport R
updated 7 weeks ago by 37k • written 8 weeks ago by • 0
2
votes
3
replies
203
views
Problem with tximport IDs
tximport tx2gene rnas DESeq2 RNASeqData
8 weeks ago Maka • 0
2
votes
4
replies
214
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confused with tximport counts abundance using salmon input
RNASeq tximport
12 weeks ago Al90 • 0
0
votes
2
replies
304
views
tximport ERROR : all(file.exists(files)) is not TRUE
Linux R tximport
4 months ago nakane_clan • 0
2
votes
5
replies
336
views
from kallisto to deseq2 analysis
biomaRt DESeq2 tximport
4 months ago Marianna • 0
2
votes
3
replies
263
views
Import RSEM output without sample data
DESeq2 tximportData tximport
updated 4 months ago by 37k • written 4 months ago by • 0
0
votes
1
reply
171
views
tximport
salmon tximport
updated 5 months ago by 37k • written 5 months ago by • 0
0
votes
1
reply
206
views
Ensembl dataset version
tximport rna rnaseqGene biomaRt
updated 5 months ago by ★ 1.3k • written 5 months ago by • 0
4
votes
3
replies
2.2k
views
tximport error: all(names(aveLengthSampGene) == rownames(lengthMat)) is not TRUE
tximport salmon R bioconductor
updated 6 months ago by • 0 • written 5.0 years ago by • 0
1
vote
4
replies
636
views
tximport from Galaxy output
normalization tximport
updated 6 months ago by • 0 • written 3.0 years ago by ▴ 10
0
votes
3
replies
432
views
tximport question on what counts to use for LogFC calculations
tximport
updated 7 months ago by 37k • written 7 months ago by • 0
0
votes
4
replies
532
views
Filtering output from tximport
tximport Salmon
updated 7 months ago by 37k • written 7 months ago by • 0
1
vote
3
replies
649
views
tximport error: all(txId == raw[[txIdCol]]) is not TRUE
tximport
8 months ago • updated 7 months ago nicolette.sipperly • 0
0
votes
3
replies
352
views
tximport cannot inport RSEM FPKM data
tximport
updated 7 months ago by 37k • written 2.0 years ago by • 0
0
votes
1
reply
478
views
tximport samples with separate tx2gene maps
tximport
updated 7 months ago by 37k • written 8 months ago by • 0
0
votes
7
replies
1.7k
views
Error reading kallisto files using tximport for cross species RNA-Seq analysis
kallisto tximport RNA-Seq across species
updated 8 months ago by • 0 • written 5.1 years ago by ▴ 40
2
votes
1
reply
302
views
How to normalize Kallisto count matrix collapsed at gene-level with TMM/DESeq2?
DESeq2 tximport Kallisto TMM edgeR
updated 8 months ago by 37k • written 8 months ago by • 0
6
votes
2
replies
5.5k
views
Using RSEM with tximport and DESeq2
deseq2 tximport software error bug
updated 9 months ago by 37k • written 5.4 years ago by • 0
0
votes
2
replies
408
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 10 months ago by 37k • written 10 months ago by • 0
1
vote
2
replies
326
views
tximeta countsFromAbundance for downstream analysis
tximeta tximport
11 months ago paulimer • 0
2
votes
3
replies
432
views
importing RSEM isoform to Gene Name with tximport
tximport
updated 12 months ago by 60k • written 12 months ago by ▴ 10
2
votes
2
replies
334
views
Issues with Tximport
tximport
12 months ago bryce.thomas • 0
0
votes
5
replies
527
views
Tximport/DESeq2 Normalization Process
tximport Normalization DESeq2
updated 12 months ago by 37k • written 13 months ago by • 0
0
votes
3
replies
595
views
Tximport error message - colnames
tximport
updated 12 months ago by 37k • written 13 months ago by • 0
4
votes
3
replies
505
views
Concatenating expression counts from different RNA-seq quantification tools
tximport HERVs edgeR DESeq2
updated 13 months ago by 37k • written 13 months ago by ▴ 30
0
votes
1
reply
363
views
Multi-factor Analysis in DeSEQ2
tximport R tximportData RNASeq DESeq2
updated 13 months ago by 37k • written 13 months ago by • 0
0
votes
6
replies
509
views
Problem with Tximport to DESeq2
TxDb.Mmusculus.UCSC.mm10.ensGene DESeq2 tximport
14 months ago zli1 • 0
1
vote
7
replies
869
views
tximport from RSEM expected counts: is it possible to import from a table rather than a file?
tximport limma rnaseq
updated 15 months ago by • 0 • written 2.1 years ago by ▴ 50
2
votes
2
replies
385
views
TxImport when quant.sf files have different index files
tximport DESeq2
15 months ago mprnl • 0
0
votes
1
reply
384
views
tximport rowsum error
tximport
16 months ago Ezgi ▴ 30
0
votes
1
reply
504
views
DESeq2, tximport normalization, normalization factors, size factors
tximport DESeq2 normalizationfactors sizefactors
updated 16 months ago by 37k • written 16 months ago by • 0
0
votes
2
replies
363
views
Pair-wise DESeq2 using tximport (running time and multi-threading)
tximport DESeq2
updated 16 months ago by 37k • written 16 months ago by • 0
1
vote
2
replies
662
views
Regarding transcripts to gene ID conversion in tximport
salmon tximport DESeq2
16 months ago Nikolay Ivanov • 0
1
vote
2
replies
1.2k
views
Importing data into the DESeq2 pipeline using tximport
DESeq2 tximport
16 months ago Nikolay Ivanov • 0
0
votes
2
replies
365
views
tximport no counts from abundance using EnsDb.Hsapiens.v86
salmon EnsDb.Hsapiens.v86 tximport
updated 17 months ago by 60k • written 17 months ago by • 0
0
votes
7
replies
719
views
Problem with Tximport
tximportData tximport
17 months ago agoesmartini • 0
3
votes
5
replies
2.0k
views
txImport: a gene seems missing from the sample data
txImportData txImport
updated 17 months ago by 60k • written 5.3 years ago by • 0
0
votes
1
reply
343
views
tximport error importing expected counts file from RSEM
RSEM tximport
updated 18 months ago by 37k • written 18 months ago by • 0
0
votes
5
replies
475
views
sumarizeToGene is dropping transcripts, how to debug
sumarizeToGene tximport
updated 18 months ago by 37k • written 19 months ago by ▴ 20
2
votes
1
reply
735
views
DESeq usage of transcript TPM after tximport
tximport
updated 18 months ago by 37k • written 18 months ago by • 0
2
votes
1
reply
428
views
tximport with salmon bootstraps and edger/deseq2
tximport
updated 18 months ago by 37k • written 18 months ago by • 0
5
votes
6
replies
969
views
Transformation of raw RSEM gene expression estimates with variance stabilizing transformation and tximport R package
DESeq2 VST rsem tximport
19 months ago svlachavas ▴ 800
0
votes
1
reply
395
views
How to use tx import on output of abundance file
tximportData tximport
updated 19 months ago by 3.6k • written 19 months ago by • 0
1
vote
4
replies
474
views
tximport abundanceCol parameter not functioning for rsem data
tximport rsem transcript abundance TPM FPKM
updated 20 months ago by 37k • written 21 months ago by • 0
0
votes
1
reply
514
views
importing RSEM data into DESeq2
deseq2 tximport
updated 20 months ago by 37k • written 20 months ago by ▴ 10
1
vote
9
replies
626
views
Question: Error running summarizeToGene() - RNA Seq Bioconductor pipeline
tximeta tximport deseq2
updated 21 months ago by 37k • written 21 months ago by ▴ 20
50 results • Page 1 of 1
Recent ...
Replies
Comment: How to get DESeq2 results for a list of genes by ATpoint ★ 1.3k
That's a problem related to your lack of R basics, neither DESeq2 or Bioconductor software/technical problem. Please learn R basics first. …
Comment: How to get DESeq2 results for a list of genes by Lucía ▴ 10
Hi, thank you! Unfortunately that doesn't work. The first option gives me this error: ``` # Extracting for list my_genes <- read.delim("di…
Answer: Error by ATpoint ★ 1.3k
https://github.com/conda-forge/rpy2-feedstock/issues/1
Comment: Error: BiocParallel errors by lxl13260684135 • 0
I came across the same problem, have you solved it?
Answer: How to get DESeq2 results for a list of genes by ATpoint ★ 1.3k
Standard rules apply for filtering in R. If the genes are the rownames of the results object `res` then: res[my_ges,] or if the colu…
Votes
A: DESeq2 interaction term in two-factor design, which contrasts?
A: DESeq2 interaction term in two-factor design, which contrasts?
DESeq2 interaction term in two-factor design, which contrasts?
DESeq2 interaction term in two-factor design, which contrasts?
Comment: How to get DESeq2 results for a list of genes
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