Showing : tximeta • reset
0
votes
4
replies
153
views
Alternative for wininet method in tximeta
DESeq2 tximport tximportData tximeta
6 weeks ago uhlkatie • 0
5
votes
9
replies
430
views
Questions regarding failing tximeta import for swish
swish fishpond GenomicFeatures tximeta
updated 12 days ago by 37k • written 4 months ago by • 0
1
vote
1
reply
240
views
Swish with more than two conditions. Add support for contrasts?
tximeta DESeq2 swish fishpond
updated 6 months ago by 37k • written 6 months ago by • 0
0
votes
1
reply
248
views
Analyzing RNA-seq data with DESeq2 Tutorial - tximeta Package Causing Error in UseMethod("filter_")
tximeta UseMethod("filter_") DESeq2
updated 8 months ago by 37k • written 8 months ago by • 0
0
votes
15
replies
1.3k
views
Tximeta Error: lexical error: invalid char in json text.
tximeta
8 months ago atariw ▴ 10
3
votes
5
replies
515
views
Error when using summarizeToGene with tximeta input for DESeq2 analysis
tximeta SummarizedExperiment DESeq2
updated 9 months ago by 37k • written 9 months ago by • 0
6
votes
10
replies
602
views
rnaseqGene: Different output when generating step by step airway dataset
tximeta DESeq2 rnaseqGene
updated 9 months ago by 37k • written 9 months ago by ▴ 20
0
votes
1
reply
384
views
Error in makeTxDbFromGFF(txomeInfo$gtf)
tximeta
updated 11 months ago by 37k • written 11 months ago by • 0
1
vote
2
replies
373
views
tximeta countsFromAbundance for downstream analysis
tximeta tximport
12 months ago paulimer • 0
3
votes
3
replies
364
views
tximeta throws error when combining Salmon outputs from multiple datasets
tximeta
13 months ago Matthias Munz ▴ 10
1
vote
1
reply
586
views
Using tximeta::summarizeToGene function; Warning message: call dbDisconnect() when finished working with a connection
tximeta
updated 14 months ago by 37k • written 14 months ago by • 0
0
votes
6
replies
576
views
Running swish on a non-reference transcript assembly / tximeta import issue
tximeta swish fishpond
updated 15 months ago by 37k • written 15 months ago by • 0
2
votes
1
reply
385
views
tximeta Error in UseMethod("filter_")
tximeta
updated 16 months ago by 37k • written 16 months ago by ▴ 30
0
votes
2
replies
499
views
Failure to save txDb using saveDb in BiocFileCache location other than /tmp
tximeta BiocFileCache
updated 16 months ago by 37k • written 16 months ago by • 0
0
votes
3
replies
489
views
Issue loading data with tximeta
tximeta
updated 16 months ago by 3.6k • written 16 months ago by • 0
0
votes
6
replies
590
views
Unexpected gene polymorphism using Salmon-tximeta-DESeq2
tximeta DESeq2
19 months ago Ray • 0
3
votes
9
replies
982
views
summarizeToGene from tximeta: not all 'rnames' found or unique.
RNA-seq tximeta
20 months ago Pufall, Miles A ▴ 30
1
vote
9
replies
665
views
Question: Error running summarizeToGene() - RNA Seq Bioconductor pipeline
tximeta tximport deseq2
updated 22 months ago by 37k • written 22 months ago by ▴ 20
1
vote
1
reply
351
views
Error in importing Salmon quantification to R using tximeta
deseq2 tximeta
updated 2.0 years ago by 37k • written 2.0 years ago by ▴ 10
1
vote
1
reply
396
views
Specifying tx2gene with tximeta
tximeta tximport
updated 2.1 years ago by 37k • written 2.1 years ago by • 0
1
vote
2
replies
353
views
RNA Seq from MusMusculus and HomoSapiens
tximeta tximport annotation
updated 2.1 years ago by 37k • written 2.1 years ago by • 0
5
votes
7
replies
801
views
tximeta - problem importing salmon files
tximeta deseq2
updated 2.1 years ago by 37k • written 2.1 years ago by • 0
1
vote
3
replies
661
views
tximeta on STAR-aligned Salmon-quantified output
tximeta salmon STAR
updated 2.3 years ago by 37k • written 2.3 years ago by ▴ 10
4
votes
0
replies
1.1k
views
Tutorial: How to post Salmon data to GEO for use with tximeta
salmon tximeta Tutorial
2.3 years ago Michael Love 37k
1
vote
2
replies
617
views
Is this an issue? "Error in (function (x) : attempt to apply non-function" when calling tximeta::summarizeToGene(se) for the first time with some da…
software error tximeta
updated 2.3 years ago by 37k • written 2.3 years ago by • 0
2
votes
12
replies
721
views
BioFileCache Problem and not linking to ensembldb problem in TxiMeta
Tximeta BioFileCache Ensembldb
updated 2.5 years ago by 25k • written 2.5 years ago by ▴ 20
0
votes
7
replies
412
views
tximeta doesn't work downloading the ref genome
deseq2 tximeta tximport rnaseq
2.5 years ago rafaelsolersanblas ▴ 50
0
votes
2
replies
465
views
Couldn't find matching transcriptome
tximeta
updated 2.5 years ago by 37k • written 2.6 years ago by • 0
0
votes
6
replies
543
views
DB file sqlite not found
tximeta sqlite
updated 2.6 years ago by 25k • written 2.6 years ago by • 0
0
votes
5
replies
487
views
importing salmon rnaseq quant with tximeta
tximeta salmon deseq2
2.6 years ago omid.alamdari • 0
3
votes
2
replies
869
views
tximeta error in fetching genome info
rnaseq tximeta
updated 2.7 years ago by 37k • written 2.7 years ago by ▴ 10
2
votes
11
replies
1.7k
views
Cannot find header.json in salmon index directory
salmon tximeta rna-seq
2.8 years ago • updated 2.7 years ago mico • 0
0
votes
4
replies
432
views
tximeta doesn't match gencode M23 transcripts to gtf
tximeta
updated 2.7 years ago by 37k • written 2.7 years ago by • 0
5
votes
6
replies
1.7k
views
How to build and map to a "pre-mRNA" reference transcriptome for single nucleus RNA-seq data?
tximeta ensembldb single-cell snRNA-seq tximport
updated 2.8 years ago by ★ 2.9k • written 2.8 years ago by ▴ 80
2
votes
3
replies
730
views
tximport::summarizeToGene fails to ignoreTxVersion
tximport tximeta AnnotationDbi
3.1 years ago Benjamin • 0
0
votes
2
replies
428
views
error in addIds
tximeta
3.3 years ago anna.sawicka • 0
2
votes
1
reply
566
views
tximeta remote versus local reference files
tximeta
updated 3.8 years ago by 37k • written 3.8 years ago by ▴ 40
37 results • Page 1 of 1
Recent ...
Replies
Comment: DEXseq error unable to find an inherited method for function NSBS for signature by ta_awwad ▴ 10
Hi there, did you manage to solve this problem? thanks TA
Comment: Error in Create switchAnalyzeRlist by k.vitting.seerup ▴ 120
I just double checked and the fasta files found [here][1] should work. Please also take a look at [this][2] if you want to use Ensembl. …
Answer: Correlation between two different datasets: between results of RNAseq and absenc by Michael Love 37k
Re: LFC, if you are working with this and then downstream analysis, I'd recommend `lfcShrink` if you aren't already using this. It will shr…
Answer: Strange Dispersion plot by Michael Love 37k
This indeed looks strange, I would immediately suspect some weird batch effects. Try all kinds of diagnostic plots like, boxplot, PCA, corr…
Answer: Correlation between CpG methylation and gene expression from DESeq2-> Normalizat by Michael Love 37k
In this case, can you say why you want to normalize for gene length? In our tximport/tximeta pipeline, it would correct for differential ge…
Votes
Answer: Error in Create switchAnalyzeRlist
Answer: Error in Create switchAnalyzeRlist
A: DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Ge
DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Gene symbol
Answer: the difference between getGEO and getGEOSuppFiles
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