Showing : tximeta • reset
0
votes
4
replies
369
views
Tximeta error in analysis of downloaded data
tximeta
5 months ago 真妃 • 0
1
vote
2
replies
322
views
summarizeToGene in tximeta causing vastly different results
DESeq2 deseq txime tximeta
updated 5 months ago by 40k • written 5 months ago by • 0
2
votes
2
replies
283
views
tximeta not yet aware of new Gencode release (Mouse M32)
tximeta
updated 7 months ago by 40k • written 7 months ago by ▴ 10
1
vote
2
replies
415
views
collapseReplicates error after tximeta
fishpond tximeta DESeq2
7 months ago Rihards Saksis • 0
1
vote
11
replies
1.2k
views
Use local Txome database to avoid downloading GTF from FTP server
tximeta
updated 11 months ago by 40k • written 11 months ago by • 0
0
votes
2
replies
624
views
How to fix warning in makeTxDbFromGFF() when using Gencode M30 (mouse)?
GenomicFeatures AnnotationHubData tximeta
updated 12 months ago by 40k • written 12 months ago by ▴ 10
0
votes
3
replies
669
views
Generate Heatmap from Gene Names after DESEQ2
DESeq2 DESEQ2 tximeta SummarizedExperiment heatmaps
updated 12 months ago by 63k • written 12 months ago by • 0
1
vote
2
replies
488
views
Error with tximeta
tximeta
updated 13 months ago by 40k • written 13 months ago by ▴ 10
0
votes
4
replies
737
views
Alternative for wininet method in tximeta
DESeq2 tximport tximportData tximeta
15 months ago uhlkatie • 0
5
votes
9
replies
1.2k
views
Questions regarding failing tximeta import for swish
swish fishpond GenomicFeatures tximeta
updated 13 months ago by 40k • written 17 months ago by • 0
1
vote
1
reply
707
views
Swish with more than two conditions. Add support for contrasts?
tximeta DESeq2 swish fishpond
updated 20 months ago by 40k • written 20 months ago by ▴ 20
0
votes
1
reply
586
views
Analyzing RNA-seq data with DESeq2 Tutorial - tximeta Package Causing Error in UseMethod("filter_")
tximeta UseMethod("filter_") DESeq2
updated 21 months ago by 40k • written 21 months ago by • 0
0
votes
15
replies
2.9k
views
Tximeta Error: lexical error: invalid char in json text.
tximeta
22 months ago atariw ▴ 10
3
votes
5
replies
1.1k
views
Error when using summarizeToGene with tximeta input for DESeq2 analysis
tximeta SummarizedExperiment DESeq2
updated 22 months ago by 40k • written 23 months ago by • 0
6
votes
10
replies
1.1k
views
rnaseqGene: Different output when generating step by step airway dataset
tximeta DESeq2 rnaseqGene
updated 22 months ago by 40k • written 22 months ago by ▴ 20
0
votes
1
reply
758
views
Error in makeTxDbFromGFF(txomeInfo$gtf)
tximeta
updated 2.0 years ago by 40k • written 2.0 years ago by • 0
1
vote
2
replies
998
views
tximeta countsFromAbundance for downstream analysis
tximeta tximport
2.1 years ago paulimer • 0
3
votes
3
replies
695
views
tximeta throws error when combining Salmon outputs from multiple datasets
tximeta
2.2 years ago Matthias Munz ▴ 10
1
vote
1
reply
1.0k
views
Using tximeta::summarizeToGene function; Warning message: call dbDisconnect() when finished working with a connection
tximeta
updated 2.3 years ago by 40k • written 2.3 years ago by • 0
0
votes
6
replies
1.0k
views
Running swish on a non-reference transcript assembly / tximeta import issue
tximeta swish fishpond
updated 2.4 years ago by 40k • written 2.4 years ago by • 0
2
votes
1
reply
652
views
tximeta Error in UseMethod("filter_")
tximeta
updated 2.4 years ago by 40k • written 2.4 years ago by ▴ 30
0
votes
2
replies
950
views
Failure to save txDb using saveDb in BiocFileCache location other than /tmp
tximeta BiocFileCache
updated 2.5 years ago by 40k • written 2.5 years ago by • 0
0
votes
3
replies
973
views
Issue loading data with tximeta
tximeta
updated 2.5 years ago by 3.8k • written 2.5 years ago by • 0
0
votes
6
replies
975
views
Unexpected gene polymorphism using Salmon-tximeta-DESeq2
tximeta DESeq2
2.7 years ago Ray ▴ 20
3
votes
9
replies
1.7k
views
summarizeToGene from tximeta: not all 'rnames' found or unique.
RNA-seq tximeta
2.8 years ago Pufall, Miles A ▴ 30
1
vote
9
replies
1.1k
views
Question: Error running summarizeToGene() - RNA Seq Bioconductor pipeline
tximeta tximport deseq2
updated 3.0 years ago by 40k • written 3.0 years ago by ▴ 20
1
vote
1
reply
639
views
Error in importing Salmon quantification to R using tximeta
deseq2 tximeta
updated 3.1 years ago by 40k • written 3.1 years ago by ▴ 10
1
vote
1
reply
734
views
Specifying tx2gene with tximeta
tximeta tximport
updated 3.2 years ago by 40k • written 3.2 years ago by • 0
1
vote
2
replies
596
views
RNA Seq from MusMusculus and HomoSapiens
tximeta tximport annotation
updated 3.2 years ago by 40k • written 3.2 years ago by • 0
5
votes
7
replies
1.5k
views
tximeta - problem importing salmon files
tximeta deseq2
updated 3.2 years ago by 40k • written 3.2 years ago by • 0
1
vote
3
replies
1.2k
views
tximeta on STAR-aligned Salmon-quantified output
tximeta salmon STAR
updated 3.4 years ago by 40k • written 3.4 years ago by ▴ 10
4
votes
0
replies
1.6k
views
Tutorial: How to post Salmon data to GEO for use with tximeta
salmon tximeta Tutorial
3.4 years ago Michael Love 40k
1
vote
2
replies
1.1k
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 3.4 years ago by 40k • written 3.4 years ago by ▴ 10
2
votes
12
replies
1.3k
views
BioFileCache Problem and not linking to ensembldb problem in TxiMeta
Tximeta BioFileCache Ensembldb
updated 3.6 years ago by 25k • written 3.6 years ago by ▴ 30
0
votes
7
replies
824
views
tximeta doesn't work downloading the ref genome
deseq2 tximeta tximport rnaseq
3.6 years ago rafaelsolersanblas ▴ 50
0
votes
2
replies
920
views
Couldn't find matching transcriptome
tximeta
updated 3.7 years ago by 40k • written 3.7 years ago by • 0
0
votes
6
replies
1.3k
views
DB file sqlite not found
tximeta sqlite
updated 3.7 years ago by 25k • written 3.7 years ago by • 0
0
votes
5
replies
921
views
importing salmon rnaseq quant with tximeta
tximeta salmon deseq2
3.7 years ago omid.alamdari • 0
3
votes
2
replies
1.2k
views
tximeta error in fetching genome info
rnaseq tximeta
updated 3.8 years ago by 40k • written 3.8 years ago by ▴ 10
2
votes
11
replies
2.5k
views
Cannot find header.json in salmon index directory
salmon tximeta rna-seq
3.9 years ago • updated 3.8 years ago mico • 0
0
votes
4
replies
728
views
tximeta doesn't match gencode M23 transcripts to gtf
tximeta
updated 3.8 years ago by 40k • written 3.8 years ago by ▴ 10
5
votes
6
replies
2.6k
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 4.0 years ago by ★ 3.0k • written 4.0 years ago by ▴ 80
2
votes
3
replies
1.5k
views
tximport::summarizeToGene fails to ignoreTxVersion
tximport tximeta AnnotationDbi
4.2 years ago Benjamin • 0
0
votes
2
replies
635
views
error in addIds
tximeta
4.4 years ago anna.sawicka • 0
2
votes
1
reply
795
views
tximeta remote versus local reference files
tximeta
updated 4.9 years ago by 40k • written 4.9 years ago by ▴ 40
45 results • Page 1 of 1
Recent ...
Replies
Comment: LIMMA dupcor() function time issue. by Gordon Smyth 48k
That's ok, but there is nothing to be gained by subsetting 1000 times. It would be better to simply subset 100,000 rows once, although the …
Comment: Specifying evidence channels in STRINGdb by robynne.braun • 0
Also I found prior thread here addressing the same question with response that functionality will be supported someday. This was a few year…
Comment: Problems with FLOWAI by SHASHI • 0
please try this using short path name and keeping your fcs file and wsp file in your local directory https://youtu.be/xLeqE7PNYzA
Comment: DataFrame Construction With Non-standard Column by Hervé Pagès 16k
SimpleList is a List derivative and List derivatives in general don't need protection. For example, a GRangesList object (which is also a L…
Answer: Deseq2, how to model design for comparing Mutant mouse at age 14 days versus Mu by swbarnes2 ★ 1.3k
The Status grouping you show above is good to use if you want to simply compare one subset of samples to another subset. The ~Genotype +…
Votes
Answer: Deseq2, enrichGO and ensembl ID
A: LIMMA dupcor() function time issue.
A: LIMMA dupcor() function time issue.
Answer: Further analysis after limma regression output
A: collapseReplicates in DESeq2
Awards • All
Popular Question to Bogdan ▴ 660
Popular Question to Michael Love 40k
Scholar to James W. MacDonald 63k
Popular Question to Theo • 0
Popular Question to Wolfgang Huber 13k
Locations • All
Germany, 9 minutes ago
United States, 18 minutes ago
WEHI, Melbourne, Australia, 25 minutes ago
United States, 28 minutes ago
United States, 29 minutes ago
Traffic: 408 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6