Showing : tximeta • reset
0
votes
11
replies
571
views
Problems with oarfish + tximport + swish
fishpond tximport tximeta
updated 12 hours ago by • 0 • written 5 days ago by • 0
0
votes
8
replies
1.1k
views
Error running tximeta
tximeta
updated 5 months ago by ★ 4.1k • written 6 months ago by • 0
0
votes
2
replies
563
views
Which fasta files to use for tximeta makeLinkTxome
tximeta DESeq2
12 months ago JING • 0
0
votes
1
reply
978
views
tximeta errors: couldn't find matching transcriptome, returning non-ranged SummarizedExperiment AND unable to find an inherited method for function '…
tximeta
updated 14 months ago by 43k • written 14 months ago by • 0
1
vote
2
replies
1.0k
views
AnnotationHub data for Mus musculus seems to be missing, while previously it was there
tximeta AnnotationHub AnnotationHubData
15 months ago Thon • 0
1
vote
2
replies
831
views
tximeta error with vroom
tximeta vroom
15 months ago Pufall, Miles A ▴ 30
0
votes
4
replies
1.1k
views
Tximeta error in analysis of downloaded data
tximeta
21 months ago 真妃 • 0
1
vote
2
replies
952
views
summarizeToGene in tximeta causing vastly different results
DESeq2 deseq txime tximeta
updated 21 months ago by 43k • written 21 months ago by • 0
2
votes
2
replies
772
views
tximeta not yet aware of new Gencode release (Mouse M32)
tximeta
updated 23 months ago by 43k • written 23 months ago by ▴ 10
1
vote
3
replies
1.1k
views
collapseReplicates error after tximeta
fishpond tximeta DESeq2
updated 16 months ago by 43k • written 23 months ago by • 0
1
vote
11
replies
2.3k
views
Use local Txome database to avoid downloading GTF from FTP server
tximeta
updated 2.2 years ago by 43k • written 2.2 years ago by • 0
0
votes
2
replies
1.4k
views
How to fix warning in makeTxDbFromGFF() when using Gencode M30 (mouse)?
GenomicFeatures AnnotationHubData tximeta
updated 2.3 years ago by 43k • written 2.3 years ago by ▴ 10
0
votes
3
replies
1.7k
views
Generate Heatmap from Gene Names after DESEQ2
DESeq2 DESEQ2 tximeta SummarizedExperiment heatmaps
updated 2.4 years ago by 67k • written 2.4 years ago by • 0
1
vote
2
replies
1.0k
views
Error with tximeta
tximeta
updated 2.4 years ago by 43k • written 2.4 years ago by ▴ 10
0
votes
4
replies
1.5k
views
Alternative for wininet method in tximeta
DESeq2 tximport tximportData tximeta
2.6 years ago uhlkatie • 0
5
votes
9
replies
2.0k
views
Questions regarding failing tximeta import for swish
swish fishpond GenomicFeatures tximeta
updated 2.5 years ago by 43k • written 2.8 years ago by • 0
1
vote
1
reply
1.3k
views
Swish with more than two conditions. Add support for contrasts?
tximeta DESeq2 swish fishpond
updated 3.0 years ago by 43k • written 3.0 years ago by ▴ 20
0
votes
1
reply
1.0k
views
Analyzing RNA-seq data with DESeq2 Tutorial - tximeta Package Causing Error in UseMethod("filter_")
tximeta UseMethod("filter_") DESeq2
updated 3.1 years ago by 43k • written 3.1 years ago by • 0
0
votes
15
replies
4.5k
views
Tximeta Error: lexical error: invalid char in json text.
tximeta
3.1 years ago atariw ▴ 10
3
votes
5
replies
2.0k
views
Error when using summarizeToGene with tximeta input for DESeq2 analysis
tximeta SummarizedExperiment DESeq2
updated 3.2 years ago by 43k • written 3.2 years ago by • 0
6
votes
10
replies
1.8k
views
rnaseqGene: Different output when generating step by step airway dataset
tximeta DESeq2 rnaseqGene
updated 3.2 years ago by 43k • written 3.2 years ago by ▴ 20
0
votes
1
reply
1.1k
views
Error in makeTxDbFromGFF(txomeInfo$gtf)
tximeta
updated 3.3 years ago by 43k • written 3.3 years ago by • 0
1
vote
2
replies
1.6k
views
tximeta countsFromAbundance for downstream analysis
tximeta tximport
3.5 years ago paulimer • 0
3
votes
3
replies
1.2k
views
tximeta throws error when combining Salmon outputs from multiple datasets
tximeta
3.5 years ago Matthias Munz ▴ 20
1
vote
1
reply
1.5k
views
Using tximeta::summarizeToGene function; Warning message: call dbDisconnect() when finished working with a connection
tximeta
updated 3.6 years ago by 43k • written 3.6 years ago by • 0
0
votes
6
replies
1.7k
views
Running swish on a non-reference transcript assembly / tximeta import issue
tximeta swish fishpond
updated 3.7 years ago by 43k • written 3.7 years ago by • 0
2
votes
1
reply
1.0k
views
tximeta Error in UseMethod("filter_")
tximeta
updated 3.8 years ago by 43k • written 3.8 years ago by ▴ 30
0
votes
2
replies
1.7k
views
Failure to save txDb using saveDb in BiocFileCache location other than /tmp
tximeta BiocFileCache
updated 3.8 years ago by 43k • written 3.8 years ago by • 0
0
votes
3
replies
1.6k
views
Issue loading data with tximeta
tximeta
updated 3.8 years ago by ★ 4.0k • written 3.8 years ago by • 0
0
votes
6
replies
1.7k
views
Unexpected gene polymorphism using Salmon-tximeta-DESeq2
tximeta DESeq2
4.0 years ago Ray ▴ 20
3
votes
9
replies
2.7k
views
summarizeToGene from tximeta: not all 'rnames' found or unique.
RNA-seq tximeta
4.1 years ago Pufall, Miles A ▴ 30
1
vote
9
replies
1.7k
views
Question: Error running summarizeToGene() - RNA Seq Bioconductor pipeline
tximeta tximport deseq2
updated 4.3 years ago by 43k • written 4.3 years ago by ▴ 20
1
vote
1
reply
982
views
Error in importing Salmon quantification to R using tximeta
deseq2 tximeta
updated 4.5 years ago by 43k • written 4.5 years ago by ▴ 10
1
vote
1
reply
1.4k
views
Specifying tx2gene with tximeta
tximeta tximport
updated 4.5 years ago by 43k • written 4.5 years ago by • 0
1
vote
2
replies
1.1k
views
RNA Seq from MusMusculus and HomoSapiens
tximeta tximport annotation
updated 4.5 years ago by 43k • written 4.5 years ago by • 0
5
votes
7
replies
2.3k
views
tximeta - problem importing salmon files
tximeta deseq2
updated 4.5 years ago by 43k • written 4.5 years ago by • 0
1
vote
3
replies
1.8k
views
tximeta on STAR-aligned Salmon-quantified output
tximeta salmon STAR
updated 4.7 years ago by 43k • written 4.7 years ago by ▴ 10
4
votes
0
replies
2.5k
views
Tutorial: How to post Salmon data to GEO for use with tximeta
salmon tximeta Tutorial
4.8 years ago Michael Love 43k
1
vote
2
replies
1.7k
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 4.8 years ago by 43k • written 4.8 years ago by ▴ 10
2
votes
12
replies
2.0k
views
BioFileCache Problem and not linking to ensembldb problem in TxiMeta
Tximeta BioFileCache Ensembldb
updated 4.9 years ago by 25k • written 4.9 years ago by ▴ 30
0
votes
7
replies
1.4k
views
tximeta doesn't work downloading the ref genome
deseq2 tximeta tximport rnaseq
4.9 years ago rafaelsolersanblas ▴ 50
0
votes
2
replies
1.6k
views
Couldn't find matching transcriptome
tximeta
updated 5.0 years ago by 43k • written 5.0 years ago by • 0
0
votes
6
replies
2.1k
views
DB file sqlite not found
tximeta sqlite
updated 5.0 years ago by 25k • written 5.0 years ago by • 0
0
votes
5
replies
1.6k
views
importing salmon rnaseq quant with tximeta
tximeta salmon deseq2
5.0 years ago omid.alamdari • 0
3
votes
2
replies
1.7k
views
tximeta error in fetching genome info
rnaseq tximeta
updated 5.1 years ago by 43k • written 5.1 years ago by ▴ 10
2
votes
11
replies
3.6k
views
Cannot find header.json in salmon index directory
salmon tximeta rna-seq
5.2 years ago • updated 5.1 years ago mico • 0
0
votes
4
replies
1.1k
views
tximeta doesn't match gencode M23 transcripts to gtf
tximeta
updated 5.2 years ago by 43k • written 5.2 years ago by ▴ 10
5
votes
6
replies
4.2k
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 5.3 years ago by ★ 3.4k • written 5.3 years ago by ▴ 80
2
votes
3
replies
2.4k
views
tximport::summarizeToGene fails to ignoreTxVersion
tximport tximeta AnnotationDbi
5.6 years ago • updated 5.5 years ago Benjamin • 0
0
votes
2
replies
952
views
error in addIds
tximeta
5.8 years ago anna.sawicka • 0
50 results • Page 1 of 1
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Comment: contrast matrix design for a continuous variable by dtzhu337 • 0
Hi Gordon, Thank you very much for your answer. Actually the variable X is the age, which I am also interested in. Somehow, age and V1 are…
Answer: SingleCellExperiment convenience function for metadata+expression? by Peter Hickey ▴ 740
Hi Sarah, `scuttle::makePerCellDF()` / `scuttle::makePerFeatureDF()` and `scater::ggcells()` / `scater::ggfeatures()`, which build upon th…
Comment: How to sort negative log2FC or FC in RNAseq for GSEA? by QN ▴ 10
Thank you ATpoint for your response! In the result of GSEA, like you indicated, there will be gene sets that have positive NES and gene se…
Comment: EdgeR Biological CVs by ATpoint ★ 4.6k
"Joseph" is a spam bot...
Answer: How to sort negative log2FC or FC in RNAseq for GSEA? by ATpoint ★ 4.6k
GSEA asks whether there are general shifts in gene expression towards certain terms. Hence, you would not split your results tables but ord…
Votes
How to correct for tumor purity using DESeq2 to analyze TCGA tumor sample expression.
Answer: EdgeR Biological CVs
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
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