Showing : Tximeta • reset
0
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5
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2.0k
views
compute_fasta_digest does not match Salmon index hash
tximeta
written 8 months ago by • 0
0
votes
8
replies
1.5k
views
ERCC Spike-In controls being discarded during Tximeta process:
@mikelove tximeta
updated 6 months ago by 43k • written 6 months ago by • 0
0
votes
1
reply
458
views
Best tximport quant.genes.sf
tximport tximeta Bioconductor
updated 6 months ago by ★ 5.0k • written 6 months ago by • 0
0
votes
11
replies
1.4k
views
Problems with oarfish + tximport + swish
fishpond tximport tximeta
updated 10 months ago by • 0 • written 10 months ago by • 0
0
votes
8
replies
1.8k
views
Error running tximeta
tximeta
updated 16 months ago by ★ 4.1k • written 16 months ago by • 0
0
votes
2
replies
830
views
Which fasta files to use for tximeta makeLinkTxome
tximeta DESeq2
22 months ago JING • 0
0
votes
1
reply
1.3k
views
tximeta errors: couldn't find matching transcriptome, returning non-ranged SummarizedExperiment AND unable to find an inherited method for function '…
tximeta
updated 2.1 years ago by 43k • written 2.1 years ago by • 0
1
vote
2
replies
1.5k
views
AnnotationHub data for Mus musculus seems to be missing, while previously it was there
tximeta AnnotationHub AnnotationHubData
2.1 years ago Thon • 0
1
vote
2
replies
1.2k
views
tximeta error with vroom
tximeta vroom
2.1 years ago Pufall, Miles A ▴ 30
0
votes
4
replies
1.4k
views
Tximeta error in analysis of downloaded data
tximeta
2.6 years ago 真妃 • 0
1
vote
2
replies
1.3k
views
summarizeToGene in tximeta causing vastly different results
DESeq2 deseq txime tximeta
updated 2.6 years ago by 43k • written 2.6 years ago by • 0
2
votes
2
replies
1.1k
views
tximeta not yet aware of new Gencode release (Mouse M32)
tximeta
updated 2.8 years ago by 43k • written 2.8 years ago by ▴ 10
1
vote
3
replies
1.4k
views
collapseReplicates error after tximeta
fishpond tximeta DESeq2
updated 2.2 years ago by 43k • written 2.8 years ago by • 0
1
vote
11
replies
3.0k
views
Use local Txome database to avoid downloading GTF from FTP server
tximeta
updated 3.1 years ago by 43k • written 3.1 years ago by • 0
0
votes
2
replies
1.8k
views
How to fix warning in makeTxDbFromGFF() when using Gencode M30 (mouse)?
GenomicFeatures AnnotationHubData tximeta
updated 3.2 years ago by 43k • written 3.2 years ago by ▴ 10
0
votes
3
replies
2.3k
views
Generate Heatmap from Gene Names after DESEQ2
DESeq2 DESEQ2 tximeta SummarizedExperiment heatmaps
updated 3.2 years ago by 68k • written 3.2 years ago by • 0
1
vote
2
replies
1.4k
views
Error with tximeta
tximeta
updated 3.3 years ago by 43k • written 3.3 years ago by ▴ 10
0
votes
4
replies
1.9k
views
Alternative for wininet method in tximeta
DESeq2 tximport tximportData tximeta
3.4 years ago uhlkatie • 0
5
votes
9
replies
2.5k
views
Questions regarding failing tximeta import for swish
swish fishpond GenomicFeatures tximeta
updated 3.3 years ago by 43k • written 3.7 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 4.0 years ago by 43k • written 4.0 years ago by • 0
0
votes
15
replies
5.4k
views
Tximeta Error: lexical error: invalid char in json text.
tximeta
4.0 years ago atariw ▴ 10
3
votes
5
replies
2.5k
views
Error when using summarizeToGene with tximeta input for DESeq2 analysis
tximeta SummarizedExperiment DESeq2
updated 4.1 years ago by 43k • written 4.1 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 4.1 years ago by 43k • written 4.1 years ago by ▴ 20
0
votes
1
reply
1.3k
views
Error in makeTxDbFromGFF(txomeInfo$gtf)
tximeta
updated 4.2 years ago by 43k • written 4.2 years ago by • 0
1
vote
2
replies
2.0k
views
tximeta countsFromAbundance for downstream analysis
tximeta tximport
4.3 years ago paulimer • 0
3
votes
3
replies
1.4k
views
tximeta throws error when combining Salmon outputs from multiple datasets
tximeta
4.4 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 4.5 years ago by 43k • written 4.5 years ago by • 0
0
votes
6
replies
2.1k
views
Running swish on a non-reference transcript assembly / tximeta import issue
tximeta swish fishpond
updated 4.6 years ago by 43k • written 4.6 years ago by • 0
2
votes
1
reply
1.2k
views
tximeta Error in UseMethod("filter_")
tximeta
updated 4.6 years ago by 43k • written 4.6 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 4.6 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 4.7 years ago by • 0
0
votes
6
replies
2.1k
views
Unexpected gene polymorphism using Salmon-tximeta-DESeq2
tximeta DESeq2
4.9 years ago Ray ▴ 20
3
votes
9
replies
3.2k
views
summarizeToGene from tximeta: not all 'rnames' found or unique.
RNA-seq tximeta
5.0 years ago Pufall, Miles A ▴ 30
1
vote
9
replies
2.2k
views
Question: Error running summarizeToGene() - RNA Seq Bioconductor pipeline
tximeta tximport deseq2
updated 5.2 years ago by 43k • written 5.2 years ago by ▴ 20
1
vote
1
reply
1.2k
views
Error in importing Salmon quantification to R using tximeta
deseq2 tximeta
updated 5.3 years ago by 43k • written 5.3 years ago by ▴ 10
1
vote
1
reply
1.7k
views
Specifying tx2gene with tximeta
tximeta tximport
updated 5.4 years ago by 43k • written 5.4 years ago by • 0
1
vote
2
replies
1.3k
views
RNA Seq from MusMusculus and HomoSapiens
tximeta tximport annotation
updated 5.4 years ago by 43k • written 5.4 years ago by • 0
5
votes
7
replies
2.6k
views
tximeta - problem importing salmon files
tximeta deseq2
updated 5.4 years ago by 43k • written 5.4 years ago by • 0
1
vote
3
replies
2.3k
views
tximeta on STAR-aligned Salmon-quantified output
tximeta salmon STAR
updated 5.6 years ago by 43k • written 5.6 years ago by ▴ 10
4
votes
0
replies
3.0k
views
Tutorial: How to post Salmon data to GEO for use with tximeta
salmon tximeta Tutorial
5.6 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 5.6 years ago by 43k • written 5.6 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 5.8 years ago by 25k • written 5.8 years ago by ▴ 30
0
votes
7
replies
1.7k
views
tximeta doesn't work downloading the ref genome
deseq2 tximeta tximport rnaseq
5.8 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
5.9 years ago omid.alamdari • 0
3
votes
2
replies
2.0k
views
tximeta error in fetching genome info
rnaseq tximeta
updated 6.0 years ago by 43k • written 6.0 years ago by ▴ 10
2
votes
11
replies
4.2k
views
Cannot find header.json in salmon index directory
salmon tximeta rna-seq
6.1 years ago • updated 6.0 years ago mico • 0
0
votes
4
replies
1.4k
views
tximeta doesn't match gencode M23 transcripts to gtf
tximeta
updated 6.0 years ago by 43k • written 6.0 years ago by ▴ 10
54 results • Page 1 of 2
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Comment: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Comment: problem reading bam files into nucleR by efoss ▴ 10
I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…
Answer: two questions about limma by Gordon Smyth 53k
Answered here: https://support.bioconductor.org/p/16318/
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much! will take that into consideration
Comment: Large logFC but somewhat high FDR by JKim • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments.
Votes
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
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