Showing : tximeta • reset
0
votes
5
replies
1.9k
views
compute_fasta_digest does not match Salmon index hash
tximeta
written 7 months ago by • 0
0
votes
8
replies
1.5k
views
ERCC Spike-In controls being discarded during Tximeta process:
@mikelove tximeta
updated 5 months ago by 43k • written 5 months ago by • 0
0
votes
1
reply
435
views
Best tximport quant.genes.sf
tximport tximeta Bioconductor
updated 5 months ago by ★ 5.0k • written 5 months ago by • 0
0
votes
11
replies
1.4k
views
Problems with oarfish + tximport + swish
fishpond tximport tximeta
updated 9 months ago by • 0 • written 9 months ago by • 0
0
votes
8
replies
1.8k
views
Error running tximeta
tximeta
updated 15 months ago by ★ 4.1k • written 15 months ago by • 0
0
votes
2
replies
810
views
Which fasta files to use for tximeta makeLinkTxome
tximeta DESeq2
21 months ago JING • 0
0
votes
1
reply
1.2k
views
tximeta errors: couldn't find matching transcriptome, returning non-ranged SummarizedExperiment AND unable to find an inherited method for function '…
tximeta
updated 24 months ago by 43k • written 24 months ago by • 0
1
vote
2
replies
1.4k
views
AnnotationHub data for Mus musculus seems to be missing, while previously it was there
tximeta AnnotationHub AnnotationHubData
2.0 years ago Thon • 0
1
vote
2
replies
1.1k
views
tximeta error with vroom
tximeta vroom
2.0 years ago Pufall, Miles A ▴ 30
0
votes
4
replies
1.3k
views
Tximeta error in analysis of downloaded data
tximeta
2.5 years ago 真妃 • 0
1
vote
2
replies
1.2k
views
summarizeToGene in tximeta causing vastly different results
DESeq2 deseq txime tximeta
updated 2.5 years ago by 43k • written 2.5 years ago by • 0
2
votes
2
replies
972
views
tximeta not yet aware of new Gencode release (Mouse M32)
tximeta
updated 2.7 years ago by 43k • written 2.7 years ago by ▴ 10
1
vote
3
replies
1.4k
views
collapseReplicates error after tximeta
fishpond tximeta DESeq2
updated 2.1 years ago by 43k • written 2.7 years ago by • 0
1
vote
11
replies
2.9k
views
Use local Txome database to avoid downloading GTF from FTP server
tximeta
updated 3.0 years ago by 43k • written 3.0 years ago by • 0
0
votes
2
replies
1.7k
views
How to fix warning in makeTxDbFromGFF() when using Gencode M30 (mouse)?
GenomicFeatures AnnotationHubData tximeta
updated 3.1 years ago by 43k • written 3.1 years ago by ▴ 10
0
votes
3
replies
2.2k
views
Generate Heatmap from Gene Names after DESEQ2
DESeq2 DESEQ2 tximeta SummarizedExperiment heatmaps
updated 3.1 years ago by 68k • written 3.1 years ago by • 0
1
vote
2
replies
1.3k
views
Error with tximeta
tximeta
updated 3.2 years ago by 43k • written 3.2 years ago by ▴ 10
0
votes
4
replies
1.9k
views
Alternative for wininet method in tximeta
DESeq2 tximport tximportData tximeta
3.3 years ago uhlkatie • 0
5
votes
9
replies
2.4k
views
Questions regarding failing tximeta import for swish
swish fishpond GenomicFeatures tximeta
updated 3.2 years ago by 43k • written 3.6 years ago by • 0
1
vote
1
reply
1.6k
views
Swish with more than two conditions. Add support for contrasts?
tximeta DESeq2 swish fishpond
updated 3.8 years ago by 43k • written 3.8 years ago by ▴ 20
0
votes
1
reply
1.3k
views
Analyzing RNA-seq data with DESeq2 Tutorial - tximeta Package Causing Error in UseMethod("filter_")
tximeta UseMethod("filter_") DESeq2
updated 3.9 years ago by 43k • written 3.9 years ago by • 0
0
votes
15
replies
5.3k
views
Tximeta Error: lexical error: invalid char in json text.
tximeta
3.9 years ago atariw ▴ 10
3
votes
5
replies
2.4k
views
Error when using summarizeToGene with tximeta input for DESeq2 analysis
tximeta SummarizedExperiment DESeq2
updated 4.0 years ago by 43k • written 4.0 years ago by • 0
6
votes
10
replies
2.4k
views
rnaseqGene: Different output when generating step by step airway dataset
tximeta DESeq2 rnaseqGene
updated 4.0 years ago by 43k • written 4.0 years ago by ▴ 20
0
votes
1
reply
1.3k
views
Error in makeTxDbFromGFF(txomeInfo$gtf)
tximeta
updated 4.1 years ago by 43k • written 4.1 years ago by • 0
1
vote
2
replies
1.9k
views
tximeta countsFromAbundance for downstream analysis
tximeta tximport
4.2 years ago paulimer • 0
3
votes
3
replies
1.4k
views
tximeta throws error when combining Salmon outputs from multiple datasets
tximeta
4.3 years ago Matthias Munz ▴ 20
1
vote
1
reply
1.8k
views
Using tximeta::summarizeToGene function; Warning message: call dbDisconnect() when finished working with a connection
tximeta
updated 4.4 years ago by 43k • written 4.4 years ago by • 0
0
votes
6
replies
2.0k
views
Running swish on a non-reference transcript assembly / tximeta import issue
tximeta swish fishpond
updated 4.5 years ago by 43k • written 4.5 years ago by • 0
2
votes
1
reply
1.2k
views
tximeta Error in UseMethod("filter_")
tximeta
updated 4.5 years ago by 43k • written 4.5 years ago by ▴ 30
0
votes
2
replies
2.0k
views
Failure to save txDb using saveDb in BiocFileCache location other than /tmp
tximeta BiocFileCache
updated 4.5 years ago by 43k • written 4.6 years ago by • 0
0
votes
3
replies
1.9k
views
Issue loading data with tximeta
tximeta
updated 4.6 years ago by ★ 4.0k • written 4.6 years ago by • 0
0
votes
6
replies
2.1k
views
Unexpected gene polymorphism using Salmon-tximeta-DESeq2
tximeta DESeq2
4.8 years ago Ray ▴ 20
3
votes
9
replies
3.2k
views
summarizeToGene from tximeta: not all 'rnames' found or unique.
RNA-seq tximeta
4.9 years ago Pufall, Miles A ▴ 30
1
vote
9
replies
2.1k
views
Question: Error running summarizeToGene() - RNA Seq Bioconductor pipeline
tximeta tximport deseq2
updated 5.1 years ago by 43k • written 5.1 years ago by ▴ 20
1
vote
1
reply
1.1k
views
Error in importing Salmon quantification to R using tximeta
deseq2 tximeta
updated 5.2 years ago by 43k • written 5.2 years ago by ▴ 10
1
vote
1
reply
1.6k
views
Specifying tx2gene with tximeta
tximeta tximport
updated 5.3 years ago by 43k • written 5.3 years ago by • 0
1
vote
2
replies
1.3k
views
RNA Seq from MusMusculus and HomoSapiens
tximeta tximport annotation
updated 5.3 years ago by 43k • written 5.3 years ago by • 0
5
votes
7
replies
2.6k
views
tximeta - problem importing salmon files
tximeta deseq2
updated 5.3 years ago by 43k • written 5.3 years ago by • 0
1
vote
3
replies
2.3k
views
tximeta on STAR-aligned Salmon-quantified output
tximeta salmon STAR
updated 5.5 years ago by 43k • written 5.5 years ago by ▴ 10
4
votes
0
replies
2.9k
views
Tutorial: How to post Salmon data to GEO for use with tximeta
salmon tximeta Tutorial
5.5 years ago Michael Love 43k
1
vote
2
replies
2.0k
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 5.5 years ago by 43k • written 5.5 years ago by ▴ 10
2
votes
12
replies
2.4k
views
BioFileCache Problem and not linking to ensembldb problem in TxiMeta
Tximeta BioFileCache Ensembldb
updated 5.7 years ago by 25k • written 5.7 years ago by ▴ 30
0
votes
7
replies
1.7k
views
tximeta doesn't work downloading the ref genome
deseq2 tximeta tximport rnaseq
5.7 years ago rafaelsolersanblas ▴ 50
0
votes
2
replies
1.8k
views
Couldn't find matching transcriptome
tximeta
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
0
votes
6
replies
2.6k
views
DB file sqlite not found
tximeta sqlite
updated 5.8 years ago by 25k • written 5.8 years ago by • 0
0
votes
5
replies
1.9k
views
importing salmon rnaseq quant with tximeta
tximeta salmon deseq2
5.8 years ago omid.alamdari • 0
3
votes
2
replies
1.9k
views
tximeta error in fetching genome info
rnaseq tximeta
updated 5.9 years ago by 43k • written 5.9 years ago by ▴ 10
2
votes
11
replies
4.2k
views
Cannot find header.json in salmon index directory
salmon tximeta rna-seq
6.0 years ago • updated 5.9 years ago mico • 0
0
votes
4
replies
1.4k
views
tximeta doesn't match gencode M23 transcripts to gtf
tximeta
updated 5.9 years ago by 43k • written 5.9 years ago by ▴ 10
54 results • Page 1 of 2
Recent ...
Replies
Comment: deseq2 filter the low counts by Michael Love 43k
Have you seen this part: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#pre-filtering
Comment: deseq2 filter the low counts by empty_mt • 0
Hi Michael, My matrix consists of 36 samples from 6 treatments (6 samples/ treatment), whether I adjust prefiltering parameters or not, in…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0
That works. I didn't realize what you said about HDF5 files. We always keep those and archive the MTX files. I'm able to read in the file…
Comment: DESeq2 interactions by Michael Love 43k
GPT even v4 gives pretty good answers to DESeq2 questions that are similar to those already posted on the support site. I've also noticed …
Answer: Important: Bioconductor Release 3.22 Delayed by shepherl 4.2k
We will continue with the release on Thursday October 30th. We have shifted one day as originally planned. Thank you
Votes
Answer: DESeq2 interactions
Answer: Important: Bioconductor Release 3.22 Delayed
A: Multi-level experiments in Limma
Answer: Should voomWithQualityWeights still be used when the sample-specific weights var
Answer: DESeq2 for candidate gene analysis
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