Showing : tximeta • reset
0
votes
5
replies
1.9k
views
compute_fasta_digest does not match Salmon index hash
tximeta
written 6 months ago by • 0
0
votes
8
replies
1.4k
views
ERCC Spike-In controls being discarded during Tximeta process:
@mikelove tximeta
updated 4 months ago by 43k • written 4 months ago by • 0
0
votes
1
reply
421
views
Best tximport quant.genes.sf
tximport tximeta Bioconductor
updated 5 months ago by ★ 5.0k • written 5 months ago by • 0
0
votes
11
replies
1.3k
views
Problems with oarfish + tximport + swish
fishpond tximport tximeta
updated 8 months ago by • 0 • written 8 months ago by • 0
0
votes
8
replies
1.7k
views
Error running tximeta
tximeta
updated 14 months ago by ★ 4.1k • written 14 months ago by • 0
0
votes
2
replies
795
views
Which fasta files to use for tximeta makeLinkTxome
tximeta DESeq2
20 months ago JING • 0
0
votes
1
reply
1.2k
views
tximeta errors: couldn't find matching transcriptome, returning non-ranged SummarizedExperiment AND unable to find an inherited method for function '…
tximeta
updated 23 months ago by 43k • written 23 months ago by • 0
1
vote
2
replies
1.4k
views
AnnotationHub data for Mus musculus seems to be missing, while previously it was there
tximeta AnnotationHub AnnotationHubData
24 months ago Thon • 0
1
vote
2
replies
1.1k
views
tximeta error with vroom
tximeta vroom
24 months ago Pufall, Miles A ▴ 30
0
votes
4
replies
1.3k
views
Tximeta error in analysis of downloaded data
tximeta
2.5 years ago 真妃 • 0
1
vote
2
replies
1.2k
views
summarizeToGene in tximeta causing vastly different results
DESeq2 deseq txime tximeta
updated 2.5 years ago by 43k • written 2.5 years ago by • 0
2
votes
2
replies
941
views
tximeta not yet aware of new Gencode release (Mouse M32)
tximeta
updated 2.7 years ago by 43k • written 2.7 years ago by ▴ 10
1
vote
3
replies
1.3k
views
collapseReplicates error after tximeta
fishpond tximeta DESeq2
updated 2.0 years ago by 43k • written 2.7 years ago by • 0
1
vote
11
replies
2.9k
views
Use local Txome database to avoid downloading GTF from FTP server
tximeta
updated 3.0 years ago by 43k • written 3.0 years ago by • 0
0
votes
2
replies
1.7k
views
How to fix warning in makeTxDbFromGFF() when using Gencode M30 (mouse)?
GenomicFeatures AnnotationHubData tximeta
updated 3.1 years ago by 43k • written 3.1 years ago by ▴ 10
0
votes
3
replies
2.2k
views
Generate Heatmap from Gene Names after DESEQ2
DESeq2 DESEQ2 tximeta SummarizedExperiment heatmaps
updated 3.1 years ago by 68k • written 3.1 years ago by • 0
1
vote
2
replies
1.3k
views
Error with tximeta
tximeta
updated 3.1 years ago by 43k • written 3.1 years ago by ▴ 10
0
votes
4
replies
1.8k
views
Alternative for wininet method in tximeta
DESeq2 tximport tximportData tximeta
3.3 years ago uhlkatie • 0
5
votes
9
replies
2.4k
views
Questions regarding failing tximeta import for swish
swish fishpond GenomicFeatures tximeta
updated 3.2 years ago by 43k • written 3.5 years ago by • 0
1
vote
1
reply
1.6k
views
Swish with more than two conditions. Add support for contrasts?
tximeta DESeq2 swish fishpond
updated 3.7 years ago by 43k • written 3.7 years ago by ▴ 20
0
votes
1
reply
1.2k
views
Analyzing RNA-seq data with DESeq2 Tutorial - tximeta Package Causing Error in UseMethod("filter_")
tximeta UseMethod("filter_") DESeq2
updated 3.8 years ago by 43k • written 3.8 years ago by • 0
0
votes
15
replies
5.3k
views
Tximeta Error: lexical error: invalid char in json text.
tximeta
3.9 years ago atariw ▴ 10
3
votes
5
replies
2.4k
views
Error when using summarizeToGene with tximeta input for DESeq2 analysis
tximeta SummarizedExperiment DESeq2
updated 3.9 years ago by 43k • written 3.9 years ago by • 0
6
votes
10
replies
2.3k
views
rnaseqGene: Different output when generating step by step airway dataset
tximeta DESeq2 rnaseqGene
updated 3.9 years ago by 43k • written 3.9 years ago by ▴ 20
0
votes
1
reply
1.3k
views
Error in makeTxDbFromGFF(txomeInfo$gtf)
tximeta
updated 4.1 years ago by 43k • written 4.1 years ago by • 0
1
vote
2
replies
1.9k
views
tximeta countsFromAbundance for downstream analysis
tximeta tximport
4.2 years ago paulimer • 0
3
votes
3
replies
1.4k
views
tximeta throws error when combining Salmon outputs from multiple datasets
tximeta
4.2 years ago Matthias Munz ▴ 20
1
vote
1
reply
1.7k
views
Using tximeta::summarizeToGene function; Warning message: call dbDisconnect() when finished working with a connection
tximeta
updated 4.3 years ago by 43k • written 4.3 years ago by • 0
0
votes
6
replies
2.0k
views
Running swish on a non-reference transcript assembly / tximeta import issue
tximeta swish fishpond
updated 4.4 years ago by 43k • written 4.5 years ago by • 0
2
votes
1
reply
1.2k
views
tximeta Error in UseMethod("filter_")
tximeta
updated 4.5 years ago by 43k • written 4.5 years ago by ▴ 30
0
votes
2
replies
2.0k
views
Failure to save txDb using saveDb in BiocFileCache location other than /tmp
tximeta BiocFileCache
updated 4.5 years ago by 43k • written 4.5 years ago by • 0
0
votes
3
replies
1.9k
views
Issue loading data with tximeta
tximeta
updated 4.5 years ago by ★ 4.0k • written 4.5 years ago by • 0
0
votes
6
replies
2.0k
views
Unexpected gene polymorphism using Salmon-tximeta-DESeq2
tximeta DESeq2
4.7 years ago Ray ▴ 20
3
votes
9
replies
3.2k
views
summarizeToGene from tximeta: not all 'rnames' found or unique.
RNA-seq tximeta
4.8 years ago Pufall, Miles A ▴ 30
1
vote
9
replies
2.1k
views
Question: Error running summarizeToGene() - RNA Seq Bioconductor pipeline
tximeta tximport deseq2
updated 5.0 years ago by 43k • written 5.0 years ago by ▴ 20
1
vote
1
reply
1.1k
views
Error in importing Salmon quantification to R using tximeta
deseq2 tximeta
updated 5.2 years ago by 43k • written 5.2 years ago by ▴ 10
1
vote
1
reply
1.6k
views
Specifying tx2gene with tximeta
tximeta tximport
updated 5.3 years ago by 43k • written 5.3 years ago by • 0
1
vote
2
replies
1.3k
views
RNA Seq from MusMusculus and HomoSapiens
tximeta tximport annotation
updated 5.3 years ago by 43k • written 5.3 years ago by • 0
5
votes
7
replies
2.6k
views
tximeta - problem importing salmon files
tximeta deseq2
updated 5.3 years ago by 43k • written 5.3 years ago by • 0
1
vote
3
replies
2.3k
views
tximeta on STAR-aligned Salmon-quantified output
tximeta salmon STAR
updated 5.4 years ago by 43k • written 5.4 years ago by ▴ 10
4
votes
0
replies
2.9k
views
Tutorial: How to post Salmon data to GEO for use with tximeta
salmon tximeta Tutorial
5.5 years ago Michael Love 43k
1
vote
2
replies
2.0k
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 5.5 years ago by 43k • written 5.5 years ago by ▴ 10
2
votes
12
replies
2.4k
views
BioFileCache Problem and not linking to ensembldb problem in TxiMeta
Tximeta BioFileCache Ensembldb
updated 5.6 years ago by 25k • written 5.6 years ago by ▴ 30
0
votes
7
replies
1.7k
views
tximeta doesn't work downloading the ref genome
deseq2 tximeta tximport rnaseq
5.6 years ago rafaelsolersanblas ▴ 50
0
votes
2
replies
1.8k
views
Couldn't find matching transcriptome
tximeta
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
0
votes
6
replies
2.5k
views
DB file sqlite not found
tximeta sqlite
updated 5.7 years ago by 25k • written 5.7 years ago by • 0
0
votes
5
replies
1.9k
views
importing salmon rnaseq quant with tximeta
tximeta salmon deseq2
5.7 years ago omid.alamdari • 0
3
votes
2
replies
1.9k
views
tximeta error in fetching genome info
rnaseq tximeta
updated 5.8 years ago by 43k • written 5.8 years ago by ▴ 10
2
votes
11
replies
4.1k
views
Cannot find header.json in salmon index directory
salmon tximeta rna-seq
5.9 years ago • updated 5.8 years ago mico • 0
0
votes
4
replies
1.4k
views
tximeta doesn't match gencode M23 transcripts to gtf
tximeta
updated 5.9 years ago by 43k • written 5.9 years ago by ▴ 10
54 results • Page 1 of 2
Recent ...
Replies
Comment: Help with defining groups by Phinney, Brett ▴ 10
I got it working , thank you!!!
Comment: Check removeBatchEffect effectiveness by massimo • 0
I would kindly ask for additional support. When not including the design_timepoint argument in removeBatchEffect and thus keeping the inter…
Comment: Error Loading Experiment from SimBenchData Package by ksankaran • 0
Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset? by ATpoint ★ 5.0k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by ATpoint ★ 5.0k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Votes
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Answer: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
Awards • All
Popular Question to Peter • 0
Popular Question to Travis • 0
Popular Question to James W. MacDonald 68k
Popular Question to Gordon Smyth 53k
Popular Question to shepherl 4.2k
Locations • All
United States, 7 minutes ago
United States, 13 minutes ago
Spain, 15 minutes ago
Pittsburgh, United States, 36 minutes ago
Switzerland/Allschwil/Idorsia, 1 hour ago
Traffic: 727 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