Showing : Tximeta • reset
0
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15
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3.7k
views
Tximeta Error: lexical error: invalid char in json text.
tximeta
2.4 years ago atariw ▴ 10
5
votes
6
replies
3.4k
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 4.6 years ago by ★ 3.3k • written 4.6 years ago by ▴ 80
2
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11
replies
3.0k
views
Cannot find header.json in salmon index directory
salmon tximeta rna-seq
4.5 years ago • updated 4.4 years ago mico • 0
3
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9
replies
2.2k
views
summarizeToGene from tximeta: not all 'rnames' found or unique.
RNA-seq tximeta
3.4 years ago Pufall, Miles A ▴ 30
4
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0
replies
2.1k
views
Tutorial: How to post Salmon data to GEO for use with tximeta
salmon tximeta Tutorial
4.1 years ago Michael Love 41k
2
votes
3
replies
2.0k
views
tximport::summarizeToGene fails to ignoreTxVersion
tximport tximeta AnnotationDbi
4.8 years ago Benjamin • 0
5
votes
7
replies
2.0k
views
tximeta - problem importing salmon files
tximeta deseq2
updated 3.8 years ago by 41k • written 3.8 years ago by • 0
1
vote
11
replies
1.8k
views
Use local Txome database to avoid downloading GTF from FTP server
tximeta
updated 18 months ago by 41k • written 18 months ago by • 0
0
votes
6
replies
1.7k
views
DB file sqlite not found
tximeta sqlite
updated 4.3 years ago by 25k • written 4.3 years ago by • 0
2
votes
12
replies
1.7k
views
BioFileCache Problem and not linking to ensembldb problem in TxiMeta
Tximeta BioFileCache Ensembldb
updated 4.2 years ago by 25k • written 4.2 years ago by ▴ 30
5
votes
9
replies
1.6k
views
Questions regarding failing tximeta import for swish
swish fishpond GenomicFeatures tximeta
updated 21 months ago by 41k • written 2.1 years ago by • 0
1
vote
3
replies
1.5k
views
tximeta on STAR-aligned Salmon-quantified output
tximeta salmon STAR
updated 4.0 years ago by 41k • written 4.0 years ago by ▴ 10
3
votes
2
replies
1.5k
views
tximeta error in fetching genome info
rnaseq tximeta
updated 4.4 years ago by 41k • written 4.4 years ago by ▴ 10
3
votes
5
replies
1.5k
views
Error when using summarizeToGene with tximeta input for DESeq2 analysis
tximeta SummarizedExperiment DESeq2
updated 2.5 years ago by 41k • written 2.5 years ago by • 0
6
votes
10
replies
1.5k
views
rnaseqGene: Different output when generating step by step airway dataset
tximeta DESeq2 rnaseqGene
updated 2.5 years ago by 41k • written 2.5 years ago by ▴ 20
0
votes
6
replies
1.4k
views
Running swish on a non-reference transcript assembly / tximeta import issue
tximeta swish fishpond
updated 3.0 years ago by 41k • written 3.0 years ago by • 0
1
vote
2
replies
1.4k
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 4.1 years ago by 41k • written 4.1 years ago by ▴ 10
1
vote
9
replies
1.4k
views
Question: Error running summarizeToGene() - RNA Seq Bioconductor pipeline
tximeta tximport deseq2
updated 3.6 years ago by 41k • written 3.6 years ago by ▴ 20
0
votes
3
replies
1.3k
views
Issue loading data with tximeta
tximeta
updated 3.1 years ago by ★ 3.9k • written 3.1 years ago by • 0
1
vote
2
replies
1.3k
views
tximeta countsFromAbundance for downstream analysis
tximeta tximport
2.8 years ago paulimer • 0
0
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6
replies
1.3k
views
Unexpected gene polymorphism using Salmon-tximeta-DESeq2
tximeta DESeq2
3.3 years ago Ray ▴ 20
0
votes
2
replies
1.3k
views
Failure to save txDb using saveDb in BiocFileCache location other than /tmp
tximeta BiocFileCache
updated 3.1 years ago by 41k • written 3.1 years ago by • 0
0
votes
5
replies
1.3k
views
importing salmon rnaseq quant with tximeta
tximeta salmon deseq2
4.3 years ago omid.alamdari • 0
1
vote
1
reply
1.3k
views
Using tximeta::summarizeToGene function; Warning message: call dbDisconnect() when finished working with a connection
tximeta
updated 2.9 years ago by 41k • written 2.9 years ago by • 0
0
votes
2
replies
1.2k
views
Couldn't find matching transcriptome
tximeta
updated 4.3 years ago by 41k • written 4.3 years ago by • 0
0
votes
3
replies
1.1k
views
Generate Heatmap from Gene Names after DESEQ2
DESeq2 DESEQ2 tximeta SummarizedExperiment heatmaps
updated 19 months ago by 65k • written 19 months ago by • 0
0
votes
7
replies
1.1k
views
tximeta doesn't work downloading the ref genome
deseq2 tximeta tximport rnaseq
4.2 years ago rafaelsolersanblas ▴ 50
0
votes
4
replies
1.1k
views
Alternative for wininet method in tximeta
DESeq2 tximport tximportData tximeta
22 months ago uhlkatie • 0
1
vote
1
reply
1.0k
views
Specifying tx2gene with tximeta
tximeta tximport
updated 3.8 years ago by 41k • written 3.8 years ago by • 0
0
votes
2
replies
1.0k
views
How to fix warning in makeTxDbFromGFF() when using Gencode M30 (mouse)?
GenomicFeatures AnnotationHubData tximeta
updated 19 months ago by 41k • written 19 months ago by ▴ 10
1
vote
1
reply
1.0k
views
Swish with more than two conditions. Add support for contrasts?
tximeta DESeq2 swish fishpond
updated 2.3 years ago by 41k • written 2.3 years ago by ▴ 20
2
votes
1
reply
1.0k
views
tximeta remote versus local reference files
tximeta
updated 5.5 years ago by 41k • written 5.5 years ago by ▴ 40
0
votes
4
replies
955
views
tximeta doesn't match gencode M23 transcripts to gtf
tximeta
updated 4.4 years ago by 41k • written 4.4 years ago by ▴ 10
0
votes
1
reply
936
views
Error in makeTxDbFromGFF(txomeInfo$gtf)
tximeta
updated 2.6 years ago by 41k • written 2.6 years ago by • 0
3
votes
3
replies
932
views
tximeta throws error when combining Salmon outputs from multiple datasets
tximeta
2.8 years ago Matthias Munz ▴ 10
2
votes
1
reply
861
views
tximeta Error in UseMethod("filter_")
tximeta
updated 3.0 years ago by 41k • written 3.0 years ago by ▴ 30
1
vote
1
reply
820
views
Error in importing Salmon quantification to R using tximeta
deseq2 tximeta
updated 3.8 years ago by 41k • written 3.8 years ago by ▴ 10
1
vote
2
replies
816
views
RNA Seq from MusMusculus and HomoSapiens
tximeta tximport annotation
updated 3.8 years ago by 41k • written 3.8 years ago by • 0
0
votes
1
reply
805
views
Analyzing RNA-seq data with DESeq2 Tutorial - tximeta Package Causing Error in UseMethod("filter_")
tximeta UseMethod("filter_") DESeq2
updated 2.4 years ago by 41k • written 2.4 years ago by • 0
0
votes
2
replies
804
views
error in addIds
tximeta
5.0 years ago anna.sawicka • 0
1
vote
3
replies
800
views
collapseReplicates error after tximeta
fishpond tximeta DESeq2
updated 7 months ago by 41k • written 15 months ago by • 0
1
vote
2
replies
760
views
Error with tximeta
tximeta
updated 20 months ago by 41k • written 20 months ago by ▴ 10
0
votes
4
replies
752
views
Tximeta error in analysis of downloaded data
tximeta
12 months ago 真妃 • 0
0
votes
1
reply
619
views
tximeta errors: couldn't find matching transcriptome, returning non-ranged SummarizedExperiment AND unable to find an inherited method for function '…
tximeta
updated 5 months ago by 41k • written 6 months ago by • 0
1
vote
2
replies
611
views
summarizeToGene in tximeta causing vastly different results
DESeq2 deseq txime tximeta
updated 12 months ago by 41k • written 12 months ago by • 0
1
vote
2
replies
571
views
AnnotationHub data for Mus musculus seems to be missing, while previously it was there
tximeta AnnotationHub AnnotationHubData
6 months ago Thon • 0
1
vote
2
replies
543
views
tximeta error with vroom
tximeta vroom
6 months ago Pufall, Miles A ▴ 30
2
votes
2
replies
533
views
tximeta not yet aware of new Gencode release (Mouse M32)
tximeta
updated 14 months ago by 41k • written 14 months ago by ▴ 10
0
votes
2
replies
270
views
Which fasta files to use for tximeta makeLinkTxome
tximeta DESeq2
3 months ago JING • 0
49 results • Page 1 of 1
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Replies
Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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