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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
Michael Love
40k • written 5 months ago by
akrunic
• 0
2
votes
2
replies
283
views
tximeta not yet aware of new Gencode release (Mouse M32)
tximeta
updated 7 months ago by
Michael Love
40k • written 7 months ago by
jtobias
▴ 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
Michael Love
40k • written 11 months ago by
Hasher
• 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
Michael Love
40k • written 12 months ago by
Pratik Mehta
▴ 10
0
votes
3
replies
669
views
Generate Heatmap from Gene Names after DESEQ2
DESeq2
DESEQ2
tximeta
SummarizedExperiment
heatmaps
updated 12 months ago by
James W. MacDonald
63k • written 12 months ago by
uhlkatie
• 0
1
vote
2
replies
488
views
Error with tximeta
tximeta
updated 13 months ago by
Michael Love
40k • written 13 months ago by
jtobias
▴ 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
Michael Love
40k • written 17 months ago by
jvandinter
• 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
Michael Love
40k • written 20 months ago by
jeremymsimon
▴ 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
Michael Love
40k • written 21 months ago by
dmbergau
• 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
Michael Love
40k • written 23 months ago by
alexw
• 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
Michael Love
40k • written 22 months ago by
jorgeplaza
▴ 20
0
votes
1
reply
758
views
Error in makeTxDbFromGFF(txomeInfo$gtf)
tximeta
updated 2.0 years ago by
Michael Love
40k • written 2.0 years ago by
Jag
• 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
Michael Love
40k • written 2.3 years ago by
Nikolay Ivanov
• 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
Michael Love
40k • written 2.4 years ago by
Jack Riley
• 0
2
votes
1
reply
652
views
tximeta Error in UseMethod("filter_")
tximeta
updated 2.4 years ago by
Michael Love
40k • written 2.4 years ago by
Pufall, Miles A
▴ 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
Michael Love
40k • written 2.5 years ago by
judith.risse
• 0
0
votes
3
replies
973
views
Issue loading data with tximeta
tximeta
updated 2.5 years ago by
Kevin Blighe
3.8k • written 2.5 years ago by
dshres
• 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
Michael Love
40k • written 3.0 years ago by
anthony.nash
▴ 20
1
vote
1
reply
639
views
Error in importing Salmon quantification to R using tximeta
deseq2
tximeta
updated 3.1 years ago by
Michael Love
40k • written 3.1 years ago by
June.
▴ 10
1
vote
1
reply
734
views
Specifying tx2gene with tximeta
tximeta
tximport
updated 3.2 years ago by
Michael Love
40k • written 3.2 years ago by
aimee.hanson
• 0
1
vote
2
replies
596
views
RNA Seq from MusMusculus and HomoSapiens
tximeta
tximport
annotation
updated 3.2 years ago by
Michael Love
40k • written 3.2 years ago by
guillaume.dachy
• 0
5
votes
7
replies
1.5k
views
tximeta - problem importing salmon files
tximeta
deseq2
updated 3.2 years ago by
Michael Love
40k • written 3.2 years ago by
rihards.saksis
• 0
1
vote
3
replies
1.2k
views
tximeta on STAR-aligned Salmon-quantified output
tximeta
salmon
STAR
updated 3.4 years ago by
Michael Love
40k • written 3.4 years ago by
josephbrown
▴ 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
Michael Love
40k • written 3.4 years ago by
kalavattam
▴ 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
Martin Morgan
25k • written 3.6 years ago by
kavator
▴ 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
Michael Love
40k • written 3.7 years ago by
Fei Liu
• 0
0
votes
6
replies
1.3k
views
DB file sqlite not found
tximeta
sqlite
updated 3.7 years ago by
Martin Morgan
25k • written 3.7 years ago by
rama.pranadi
• 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
Michael Love
40k • written 3.8 years ago by
MT
▴ 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
Michael Love
40k • written 3.8 years ago by
jtobias
▴ 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
Robert Castelo
★ 3.0k • written 4.0 years ago by
Stephanie Hicks
▴ 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
Michael Love
40k • written 4.9 years ago by
igor
▴ 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
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