Showing : tximeta • reset
0
votes
2
replies
261
views
Which fasta files to use for tximeta makeLinkTxome
tximeta DESeq2
3 months ago JING • 0
0
votes
1
reply
603
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 5 months ago by • 0
1
vote
2
replies
549
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
526
views
tximeta error with vroom
tximeta vroom
6 months ago Pufall, Miles A ▴ 30
1
vote
3
replies
788
views
collapseReplicates error after tximeta
fishpond tximeta DESeq2
updated 7 months ago by 41k • written 14 months ago by • 0
0
votes
4
replies
737
views
Tximeta error in analysis of downloaded data
tximeta
12 months ago 真妃 • 0
1
vote
2
replies
604
views
summarizeToGene in tximeta causing vastly different results
DESeq2 deseq txime tximeta
updated 12 months ago by 41k • written 12 months ago by • 0
2
votes
2
replies
518
views
tximeta not yet aware of new Gencode release (Mouse M32)
tximeta
updated 14 months ago by 41k • written 14 months ago by ▴ 10
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
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
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
1
vote
2
replies
744
views
Error with tximeta
tximeta
updated 20 months ago by 41k • written 20 months ago by ▴ 10
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
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
992
views
Swish with more than two conditions. Add support for contrasts?
tximeta DESeq2 swish fishpond
updated 2.2 years ago by 41k • written 2.2 years ago by ▴ 20
0
votes
1
reply
793
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
15
replies
3.7k
views
Tximeta Error: lexical error: invalid char in json text.
tximeta
2.4 years ago atariw ▴ 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
1.4k
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
1
reply
930
views
Error in makeTxDbFromGFF(txomeInfo$gtf)
tximeta
updated 2.6 years ago by 41k • written 2.6 years ago by • 0
1
vote
2
replies
1.3k
views
tximeta countsFromAbundance for downstream analysis
tximeta tximport
2.7 years ago paulimer • 0
3
votes
3
replies
917
views
tximeta throws error when combining Salmon outputs from multiple datasets
tximeta
2.8 years ago Matthias Munz ▴ 10
1
vote
1
reply
1.2k
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
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
2
votes
1
reply
851
views
tximeta Error in UseMethod("filter_")
tximeta
updated 3.0 years ago by 41k • written 3.0 years ago by ▴ 30
0
votes
2
replies
1.3k
views
Failure to save txDb using saveDb in BiocFileCache location other than /tmp
tximeta BiocFileCache
updated 3.0 years ago by 41k • written 3.0 years ago by • 0
0
votes
3
replies
1.3k
views
Issue loading data with tximeta
tximeta
updated 3.0 years ago by ★ 3.9k • written 3.1 years ago by • 0
0
votes
6
replies
1.3k
views
Unexpected gene polymorphism using Salmon-tximeta-DESeq2
tximeta DESeq2
3.3 years ago Ray ▴ 20
3
votes
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
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
1
vote
1
reply
816
views
Error in importing Salmon quantification to R using tximeta
deseq2 tximeta
updated 3.7 years ago by 41k • written 3.7 years ago by ▴ 10
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
1
vote
2
replies
808
views
RNA Seq from MusMusculus and HomoSapiens
tximeta tximport annotation
updated 3.8 years ago by 41k • written 3.8 years ago by • 0
5
votes
7
replies
1.9k
views
tximeta - problem importing salmon files
tximeta deseq2
updated 3.8 years ago by 41k • written 3.8 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
4
votes
0
replies
2.1k
views
Tutorial: How to post Salmon data to GEO for use with tximeta
salmon tximeta Tutorial
4.0 years ago Michael Love 41k
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 4.0 years ago by 41k • written 4.0 years ago by ▴ 10
2
votes
12
replies
1.6k
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
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
2
replies
1.2k
views
Couldn't find matching transcriptome
tximeta
updated 4.2 years ago by 41k • written 4.2 years ago by • 0
0
votes
6
replies
1.7k
views
DB file sqlite not found
tximeta sqlite
updated 4.2 years ago by 25k • written 4.2 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
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
2
votes
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
0
votes
4
replies
945
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
5
votes
6
replies
3.3k
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 4.5 years ago by ★ 3.3k • written 4.5 years ago by ▴ 80
2
votes
3
replies
2.0k
views
tximport::summarizeToGene fails to ignoreTxVersion
tximport tximeta AnnotationDbi
4.8 years ago Benjamin • 0
0
votes
2
replies
800
views
error in addIds
tximeta
5.0 years ago anna.sawicka • 0
2
votes
1
reply
995
views
tximeta remote versus local reference files
tximeta
updated 5.5 years ago by 41k • written 5.5 years ago by ▴ 40
49 results • Page 1 of 1
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Replies
Comment: How to retrieve gene ontology GO class from gene list? by bandconductor • 0
Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Comment: PCA plot suggestions by JKim • 0
cross post: https://www.biostars.org/p/9593486/
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
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