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Showing :
Tximeta
•
reset
0
votes
2
replies
263
views
Which fasta files to use for tximeta makeLinkTxome
tximeta
DESeq2
3 months ago
JING
• 0
0
votes
1
reply
608
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
Michael Love
41k • written 5 months ago by
kyliecode
• 0
1
vote
2
replies
552
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
529
views
tximeta error with vroom
tximeta
vroom
6 months ago
Pufall, Miles A
▴ 30
1
vote
3
replies
792
views
collapseReplicates error after tximeta
fishpond
tximeta
DESeq2
updated 7 months ago by
Michael Love
41k • written 14 months ago by
Rihards Saksis
• 0
0
votes
4
replies
740
views
Tximeta error in analysis of downloaded data
tximeta
12 months ago
真妃
• 0
1
vote
2
replies
606
views
summarizeToGene in tximeta causing vastly different results
DESeq2
deseq
txime
tximeta
updated 12 months ago by
Michael Love
41k • written 12 months ago by
akrunic
• 0
2
votes
2
replies
525
views
tximeta not yet aware of new Gencode release (Mouse M32)
tximeta
updated 14 months ago by
Michael Love
41k • written 14 months ago by
jtobias
▴ 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
Michael Love
41k • written 18 months ago by
Hasher
• 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
Michael Love
41k • written 19 months ago by
Pratik Mehta
▴ 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
James W. MacDonald
65k • written 19 months ago by
uhlkatie
• 0
1
vote
2
replies
748
views
Error with tximeta
tximeta
updated 20 months ago by
Michael Love
41k • written 20 months ago by
jtobias
▴ 10
5
votes
9
replies
1.6k
views
Questions regarding failing tximeta import for swish
swish
fishpond
GenomicFeatures
tximeta
updated 21 months ago by
Michael Love
41k • written 2.1 years ago by
jvandinter
• 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
995
views
Swish with more than two conditions. Add support for contrasts?
tximeta
DESeq2
swish
fishpond
updated 2.2 years ago by
Michael Love
41k • written 2.2 years ago by
jeremymsimon
▴ 20
0
votes
1
reply
796
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
Michael Love
41k • written 2.4 years ago by
dmbergau
• 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
Michael Love
41k • written 2.5 years ago by
alexw
• 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
Michael Love
41k • written 2.5 years ago by
jorgeplaza
▴ 20
0
votes
1
reply
931
views
Error in makeTxDbFromGFF(txomeInfo$gtf)
tximeta
updated 2.6 years ago by
Michael Love
41k • written 2.6 years ago by
Jag
• 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
920
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
Michael Love
41k • written 2.9 years ago by
Nikolay Ivanov
• 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
Michael Love
41k • written 3.0 years ago by
Jack Riley
• 0
2
votes
1
reply
853
views
tximeta Error in UseMethod("filter_")
tximeta
updated 3.0 years ago by
Michael Love
41k • written 3.0 years ago by
Pufall, Miles A
▴ 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
Michael Love
41k • written 3.0 years ago by
judith.risse
• 0
0
votes
3
replies
1.3k
views
Issue loading data with tximeta
tximeta
updated 3.1 years ago by
Kevin Blighe
★ 3.9k • written 3.1 years ago by
dshres
• 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
Michael Love
41k • written 3.6 years ago by
anthony.nash
▴ 20
1
vote
1
reply
819
views
Error in importing Salmon quantification to R using tximeta
deseq2
tximeta
updated 3.7 years ago by
Michael Love
41k • written 3.7 years ago by
June.
▴ 10
1
vote
1
reply
1.0k
views
Specifying tx2gene with tximeta
tximeta
tximport
updated 3.8 years ago by
Michael Love
41k • written 3.8 years ago by
aimee.hanson
• 0
1
vote
2
replies
811
views
RNA Seq from MusMusculus and HomoSapiens
tximeta
tximport
annotation
updated 3.8 years ago by
Michael Love
41k • written 3.8 years ago by
guillaume.dachy
• 0
5
votes
7
replies
1.9k
views
tximeta - problem importing salmon files
tximeta
deseq2
updated 3.8 years ago by
Michael Love
41k • written 3.8 years ago by
rihards.saksis
• 0
1
vote
3
replies
1.5k
views
tximeta on STAR-aligned Salmon-quantified output
tximeta
salmon
STAR
updated 4.0 years ago by
Michael Love
41k • written 4.0 years ago by
josephbrown
▴ 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
Michael Love
41k • written 4.0 years ago by
kalavattam
▴ 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
Martin Morgan
25k • written 4.2 years ago by
kavator
▴ 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
Michael Love
41k • written 4.2 years ago by
Fei Liu
• 0
0
votes
6
replies
1.7k
views
DB file sqlite not found
tximeta
sqlite
updated 4.3 years ago by
Martin Morgan
25k • written 4.3 years ago by
rama.pranadi
• 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
Michael Love
41k • written 4.4 years ago by
MT
▴ 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
948
views
tximeta doesn't match gencode M23 transcripts to gtf
tximeta
updated 4.4 years ago by
Michael Love
41k • written 4.4 years ago by
jtobias
▴ 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
Robert Castelo
★ 3.3k • written 4.5 years ago by
Stephanie Hicks
▴ 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
802
views
error in addIds
tximeta
5.0 years ago
anna.sawicka
• 0
2
votes
1
reply
997
views
tximeta remote versus local reference files
tximeta
updated 5.5 years ago by
Michael Love
41k • written 5.5 years ago by
igor
▴ 40
49 results • Page
1 of 1
Recent ...
Replies
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
pl23
• 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions
by
Michael Love
41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
ussarizona
▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative?
by
Michael Love
41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks
by
ATpoint
★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Votes
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
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