Log In
Sign Up
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
Log In
Sign Up
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
Showing :
Tximeta
•
reset
0
votes
0
replies
29
views
compute_fasta_digest does not match Salmon index hash
tximeta
3 days ago
Alex
• 0
0
votes
11
replies
814
views
Problems with oarfish + tximport + swish
fishpond
tximport
tximeta
updated 9 weeks ago by
Im
• 0 • written 10 weeks ago by
brown.annaleigh
• 0
0
votes
8
replies
1.3k
views
Error running tximeta
tximeta
updated 8 months ago by
Guido Hooiveld
★ 4.1k • written 8 months ago by
daria.igudesman
• 0
0
votes
2
replies
630
views
Which fasta files to use for tximeta makeLinkTxome
tximeta
DESeq2
14 months ago
JING
• 0
0
votes
1
reply
1.0k
views
tximeta errors: couldn't find matching transcriptome, returning non-ranged SummarizedExperiment AND unable to find an inherited method for function '…
tximeta
updated 16 months ago by
Michael Love
43k • written 17 months ago by
kyliecode
• 0
1
vote
2
replies
1.2k
views
AnnotationHub data for Mus musculus seems to be missing, while previously it was there
tximeta
AnnotationHub
AnnotationHubData
17 months ago
Thon
• 0
1
vote
2
replies
896
views
tximeta error with vroom
tximeta
vroom
17 months ago
Pufall, Miles A
▴ 30
0
votes
4
replies
1.1k
views
Tximeta error in analysis of downloaded data
tximeta
23 months ago
真妃
• 0
1
vote
2
replies
1.0k
views
summarizeToGene in tximeta causing vastly different results
DESeq2
deseq
txime
tximeta
updated 23 months ago by
Michael Love
43k • written 23 months ago by
akrunic
• 0
2
votes
2
replies
827
views
tximeta not yet aware of new Gencode release (Mouse M32)
tximeta
updated 2.1 years ago by
Michael Love
43k • written 2.1 years ago by
jtobias
▴ 10
1
vote
3
replies
1.2k
views
collapseReplicates error after tximeta
fishpond
tximeta
DESeq2
updated 18 months ago by
Michael Love
43k • written 2.1 years ago by
Rihards Saksis
• 0
1
vote
11
replies
2.5k
views
Use local Txome database to avoid downloading GTF from FTP server
tximeta
updated 2.4 years ago by
Michael Love
43k • written 2.4 years ago by
Hasher
• 0
0
votes
2
replies
1.5k
views
How to fix warning in makeTxDbFromGFF() when using Gencode M30 (mouse)?
GenomicFeatures
AnnotationHubData
tximeta
updated 2.5 years ago by
Michael Love
43k • written 2.5 years ago by
Pratik Mehta
▴ 10
0
votes
3
replies
1.9k
views
Generate Heatmap from Gene Names after DESEQ2
DESeq2
DESEQ2
tximeta
SummarizedExperiment
heatmaps
updated 2.5 years ago by
James W. MacDonald
68k • written 2.5 years ago by
uhlkatie
• 0
1
vote
2
replies
1.1k
views
Error with tximeta
tximeta
updated 2.6 years ago by
Michael Love
43k • written 2.6 years ago by
jtobias
▴ 10
0
votes
4
replies
1.6k
views
Alternative for wininet method in tximeta
DESeq2
tximport
tximportData
tximeta
2.7 years ago
uhlkatie
• 0
5
votes
9
replies
2.1k
views
Questions regarding failing tximeta import for swish
swish
fishpond
GenomicFeatures
tximeta
updated 2.7 years ago by
Michael Love
43k • written 3.0 years ago by
jvandinter
• 0
1
vote
1
reply
1.4k
views
Swish with more than two conditions. Add support for contrasts?
tximeta
DESeq2
swish
fishpond
updated 3.2 years ago by
Michael Love
43k • written 3.2 years ago by
jeremymsimon
▴ 20
0
votes
1
reply
1.1k
views
Analyzing RNA-seq data with DESeq2 Tutorial - tximeta Package Causing Error in UseMethod("filter_")
tximeta
UseMethod("filter_")
DESeq2
updated 3.3 years ago by
Michael Love
43k • written 3.3 years ago by
dmbergau
• 0
0
votes
15
replies
4.8k
views
Tximeta Error: lexical error: invalid char in json text.
tximeta
3.3 years ago
atariw
▴ 10
3
votes
5
replies
2.1k
views
Error when using summarizeToGene with tximeta input for DESeq2 analysis
tximeta
SummarizedExperiment
DESeq2
updated 3.4 years ago by
Michael Love
43k • written 3.4 years ago by
alexw
• 0
6
votes
10
replies
2.0k
views
rnaseqGene: Different output when generating step by step airway dataset
tximeta
DESeq2
rnaseqGene
updated 3.4 years ago by
Michael Love
43k • written 3.4 years ago by
jorgeplaza
▴ 20
0
votes
1
reply
1.2k
views
Error in makeTxDbFromGFF(txomeInfo$gtf)
tximeta
updated 3.5 years ago by
Michael Love
43k • written 3.5 years ago by
Jag
• 0
1
vote
2
replies
1.7k
views
tximeta countsFromAbundance for downstream analysis
tximeta
tximport
3.7 years ago • updated 3.6 years ago
paulimer
• 0
3
votes
3
replies
1.2k
views
tximeta throws error when combining Salmon outputs from multiple datasets
tximeta
3.7 years ago
Matthias Munz
▴ 20
1
vote
1
reply
1.6k
views
Using tximeta::summarizeToGene function; Warning message: call dbDisconnect() when finished working with a connection
tximeta
updated 3.8 years ago by
Michael Love
43k • written 3.8 years ago by
Nikolay Ivanov
• 0
0
votes
6
replies
1.8k
views
Running swish on a non-reference transcript assembly / tximeta import issue
tximeta
swish
fishpond
updated 3.9 years ago by
Michael Love
43k • written 3.9 years ago by
Jack Riley
• 0
2
votes
1
reply
1.1k
views
tximeta Error in UseMethod("filter_")
tximeta
updated 3.9 years ago by
Michael Love
43k • written 3.9 years ago by
Pufall, Miles A
▴ 30
0
votes
2
replies
1.8k
views
Failure to save txDb using saveDb in BiocFileCache location other than /tmp
tximeta
BiocFileCache
updated 4.0 years ago by
Michael Love
43k • written 4.0 years ago by
judith.risse
• 0
0
votes
3
replies
1.7k
views
Issue loading data with tximeta
tximeta
updated 4.0 years ago by
Kevin Blighe
★ 4.0k • written 4.0 years ago by
dshres
• 0
0
votes
6
replies
1.8k
views
Unexpected gene polymorphism using Salmon-tximeta-DESeq2
tximeta
DESeq2
4.2 years ago
Ray
▴ 20
3
votes
9
replies
2.9k
views
summarizeToGene from tximeta: not all 'rnames' found or unique.
RNA-seq
tximeta
4.3 years ago
Pufall, Miles A
▴ 30
1
vote
9
replies
1.8k
views
Question: Error running summarizeToGene() - RNA Seq Bioconductor pipeline
tximeta
tximport
deseq2
updated 4.5 years ago by
Michael Love
43k • written 4.5 years ago by
anthony.nash
▴ 20
1
vote
1
reply
1.0k
views
Error in importing Salmon quantification to R using tximeta
deseq2
tximeta
updated 4.6 years ago by
Michael Love
43k • written 4.6 years ago by
June.
▴ 10
1
vote
1
reply
1.5k
views
Specifying tx2gene with tximeta
tximeta
tximport
updated 4.7 years ago by
Michael Love
43k • written 4.7 years ago by
aimee.hanson
• 0
1
vote
2
replies
1.1k
views
RNA Seq from MusMusculus and HomoSapiens
tximeta
tximport
annotation
updated 4.7 years ago by
Michael Love
43k • written 4.7 years ago by
guillaume.dachy
• 0
5
votes
7
replies
2.4k
views
tximeta - problem importing salmon files
tximeta
deseq2
updated 4.7 years ago by
Michael Love
43k • written 4.7 years ago by
rihards.saksis
• 0
1
vote
3
replies
2.0k
views
tximeta on STAR-aligned Salmon-quantified output
tximeta
salmon
STAR
updated 4.9 years ago by
Michael Love
43k • written 4.9 years ago by
josephbrown
▴ 10
4
votes
0
replies
2.6k
views
Tutorial:
How to post Salmon data to GEO for use with tximeta
salmon
tximeta
Tutorial
5.0 years ago
Michael Love
43k
1
vote
2
replies
1.8k
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 5.0 years ago by
Michael Love
43k • written 5.0 years ago by
kalavattam
▴ 10
2
votes
12
replies
2.1k
views
BioFileCache Problem and not linking to ensembldb problem in TxiMeta
Tximeta
BioFileCache
Ensembldb
updated 5.1 years ago by
Martin Morgan
25k • written 5.1 years ago by
kavator
▴ 30
0
votes
7
replies
1.5k
views
tximeta doesn't work downloading the ref genome
deseq2
tximeta
tximport
rnaseq
5.1 years ago
rafaelsolersanblas
▴ 50
0
votes
2
replies
1.6k
views
Couldn't find matching transcriptome
tximeta
updated 5.2 years ago by
Michael Love
43k • written 5.2 years ago by
Fei Liu
• 0
0
votes
6
replies
2.3k
views
DB file sqlite not found
tximeta
sqlite
updated 5.2 years ago by
Martin Morgan
25k • written 5.2 years ago by
rama.pranadi
• 0
0
votes
5
replies
1.7k
views
importing salmon rnaseq quant with tximeta
tximeta
salmon
deseq2
5.2 years ago
omid.alamdari
• 0
3
votes
2
replies
1.8k
views
tximeta error in fetching genome info
rnaseq
tximeta
updated 5.3 years ago by
Michael Love
43k • written 5.3 years ago by
MT
▴ 10
2
votes
11
replies
3.7k
views
Cannot find header.json in salmon index directory
salmon
tximeta
rna-seq
5.4 years ago • updated 5.3 years ago
mico
• 0
0
votes
4
replies
1.2k
views
tximeta doesn't match gencode M23 transcripts to gtf
tximeta
updated 5.3 years ago by
Michael Love
43k • written 5.3 years ago by
jtobias
▴ 10
5
votes
6
replies
4.5k
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 5.5 years ago by
Robert Castelo
★ 3.4k • written 5.5 years ago by
Stephanie Hicks
▴ 80
2
votes
3
replies
2.5k
views
tximport::summarizeToGene fails to ignoreTxVersion
tximport
tximeta
AnnotationDbi
5.7 years ago
Benjamin
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: Package developing and interoperation with Bioconductor
by
slizchap
• 0
Thank you so much for your answer. This was very useful, I will optimize my functions so they can handle SE objects.
Comment: Package developing and interoperation with Bioconductor
by
slizchap
• 0
Thank you so much for your answer, very useful!
Comment: Error in H5Dclose(h5dataset) when trying to read in kallisto h5 files
by
Mike Smith
★ 6.6k
Tricky to try and debug this without some example files to work with. Can you provide the output of `traceback()` called immediately after…
Answer: Mismatch between Illumina Mouse Methylation BeadChip annotation and genome brows
by
James W. MacDonald
68k
The annotation data that is provided for this array is simply a repackaging of data that we get from Illumina, so any apparent inconsistenc…
Answer: Package developing and interoperation with Bioconductor
by
James W. MacDonald
68k
Ideally you would have S4 methods that dispatch on the incoming data structure, so people could call your main function using a `data.frame…
Votes
Comment: ComBat with repeated measures
Answer: Package developing and interoperation with Bioconductor
Answer: CpGs with genomic positions greater than the chromosome size in EPICv2?
Answer: Explannation for ROAST results
A: How DiffBind run PCA based on peak data?
Awards
• All
Popular Question
to
hrishi27n
▴ 20
Supporter
to
bhanu.chandra1
• 0
Popular Question
to
Gordon Smyth
52k
Popular Question
to
mdeea123
▴ 10
Popular Question
to
GA
▴ 10
Locations
• All
Mexico,
37 minutes ago
The city by the bay,
1 hour ago
United States,
1 hour ago
Pittsburgh, United States,
2 hours ago
Germany,
2 hours ago
Traffic: 417 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