Showing : Tximeta • reset
0
votes
2
replies
276
views
Which fasta files to use for tximeta makeLinkTxome
tximeta DESeq2
3 months ago JING • 0
0
votes
1
reply
624
views
tximeta errors: couldn't find matching transcriptome, returning non-ranged SummarizedExperiment AND unable to find an inherited method for function '…
tximeta
updated 6 months ago by 41k • written 6 months ago by • 0
1
vote
2
replies
578
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
546
views
tximeta error with vroom
tximeta vroom
6 months ago Pufall, Miles A ▴ 30
0
votes
4
replies
758
views
Tximeta error in analysis of downloaded data
tximeta
12 months ago 真妃 • 0
1
vote
2
replies
616
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
537
views
tximeta not yet aware of new Gencode release (Mouse M32)
tximeta
updated 14 months ago by 41k • written 15 months ago by ▴ 10
1
vote
3
replies
803
views
collapseReplicates error after tximeta
fishpond tximeta DESeq2
updated 7 months ago by 41k • written 15 months 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
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
1.2k
views
Generate Heatmap from Gene Names after DESEQ2
DESeq2 DESEQ2 tximeta SummarizedExperiment heatmaps
updated 19 months ago by 65k • written 20 months ago by • 0
1
vote
2
replies
767
views
Error with tximeta
tximeta
updated 20 months ago by 41k • written 20 months ago by ▴ 10
0
votes
4
replies
1.1k
views
Alternative for wininet method in tximeta
DESeq2 tximport tximportData tximeta
22 months ago uhlkatie • 0
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
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
0
votes
1
reply
807
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
1.5k
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
1
reply
937
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
2.8 years ago paulimer • 0
3
votes
3
replies
937
views
tximeta throws error when combining Salmon outputs from multiple datasets
tximeta
2.8 years ago Matthias Munz ▴ 10
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
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
863
views
tximeta Error in UseMethod("filter_")
tximeta
updated 3.1 years ago by 41k • written 3.1 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 3.1 years ago by 41k • written 3.1 years ago by • 0
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
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
823
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
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
820
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
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
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
4.1 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 4.1 years ago by 41k • written 4.1 years ago by ▴ 10
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
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 4.3 years ago by 41k • written 4.3 years 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
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
959
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
3.4k
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
votes
3
replies
2.0k
views
tximport::summarizeToGene fails to ignoreTxVersion
tximport tximeta AnnotationDbi
4.8 years ago Benjamin • 0
0
votes
2
replies
808
views
error in addIds
tximeta
5.1 years ago anna.sawicka • 0
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
49 results • Page 1 of 1
Recent ...
Replies
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
I will follow what you suggested. I didn't use max gap anywhere. I was following statistic I and regarding the size of features, my small…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 41k
Oh I see, for the second question, I don't have a great answer. I typically think of one set as the anchor, whose ascertainment is driving …
Comment: Help with running egsea() by James W. MacDonald 65k
Oh, right. Ideally you would use NCBI (aka Entrez gene) IDs because they are way more likely to be unique. Gene symbols are broken down int…
Comment: Help with running egsea() by Chris • 0
Thanks James! I update the question. The last question mean when we use `buildIdx()`, could we use gene symbol instead of entrezID. However…
Comment: Help with running egsea() by James W. MacDonald 65k
I don't understand the last question, but do look at the msigdb.gsets argument to `buildIdx` in the help page for that function.
Votes
Comment: Help with running egsea()
Answer: Trim/Filter out-of-bounds GRanges
Comment: Help with running egsea()
Answer: How to save the DEXSeq results
Answer: How to save the DEXSeq results
Awards • All
Scholar to Michael Love 41k
Popular Question to Malcolm Cook ★ 1.6k
Teacher to Gordon Smyth 50k
Popular Question to priyanka.m • 0
Popular Question to Vincent J. Carey, Jr. 6.7k
Locations • All
WEHI, Melbourne, Australia, 1 minute ago
Spain, 14 minutes ago
France, 17 minutes ago
India, 24 minutes ago
Turkey, 25 minutes ago
Traffic: 700 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