thelovelab tximeta issues

thelovelab / tximeta

Transcript quantification import with automatic metadata detection

https://thelovelab.github.io/tximeta/

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issues

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Support for `oarfish` quants

#81 mikelove closed 3 months ago
4
issue importing alevin files with tximeta 1.20.0

#80 csoneson closed 7 months ago
3
a problem after installing tximeta

#79 WesleyChan0917 closed 3 months ago
4
Add genome2UCSC mapping for GRCm39

#78 csoneson closed 9 months ago
3
Change genome build to GRCm39 for GENCODE release M26 and later

#77 csoneson closed 9 months ago
2
Issue with cache

#76 guidohooiveld closed 10 months ago
2
When disconnected still sometimes error trying to get seqinfo

#75 mikelove opened 11 months ago
0
Convert list from tximport() to SummarizedExperiment object

#74 ElvaWong closed 10 months ago
2
summarizeToGene should use most abundant isoform for GRanges

#73 mikelove closed 11 months ago
1
couldn't find matching transcriptome, returning non-ranged SummarizedExperiment (alignment mode)

#72 errcricket closed 1 year ago
4
SummarizedExperiment or DESeqDataSet Leves Null

#71 lulumagic7 closed 1 year ago
2
Error in .nextMethod(.Object, ...) : invalid names for slots of class "EnsDb": conn, packageName

#70 Yang-amd closed 1 year ago
8
GENCODE transcriptome v42 not recognised

#69 GiBacci closed 1 year ago
1
Tximeta for novel transcripts by stringite

#68 karlaarz closed 1 year ago
12
Unsuccessful connection to AnnotationHub blocks tximeta on HPC

#67 danilotat closed 1 year ago
5
Error in checkAssays2Txps

#66 karlaarz closed 2 years ago
5
GENCODE - Mus musculus - release M28 not loading ok

#65 AMChalkie closed 1 year ago
13
Getting "couldn't find matching transcriptome" with Gencode 40

#64 jwtobias closed 2 years ago
3
Salmon + GRCh38.p13: none of the transcripts in the quantification files are in the GTF

#63 ManuelArcieri closed 2 years ago
8
tximeta returns Error: lexical error: invalid string in json text.

#62 Shellfishgene closed 2 years ago
2
If skipMeta=TRUE, still could put Salmon version etc

#61 mikelove opened 2 years ago
0
Best measures for gene Fold change between pre- and post-treatment samples and for gene comparison within a sample

#60 mpunta closed 2 years ago
1
DGElist coldata

#59 csoneson closed 2 years ago
2
tximeta UCSC not co-operating in terms of mm10

#58 justinjacobse closed 2 years ago
2
Error in checkAssays2Txps(assays, txps) : none of the transcripts in the quantification files are in the GTF

#57 csgroen closed 3 years ago
6
cached transcript fails to build

#56 JudithR closed 3 years ago
9
addExons throws error: in bfcrpath(bfc, txdbName) : not all 'rnames' found or unique.

#55 matmu closed 3 years ago
2
none of the transcripts in the quantification files are in the GTF

#54 ibekere closed 3 years ago
9
dtuScaledTPM doesn't work

#53 mikelove opened 3 years ago
0
Should tximeta find any available TxDb/EnsDb when hash is identical?

#52 mikelove opened 3 years ago
0
did not find matching TxDb via 'AnnotationHub'

#51 AbbyFeng closed 3 years ago
2
couldn't find matching transcriptome, returning non-ranged SummarizedExperiment

#50 Alexander-Suen closed 3 years ago
3
Make sure loading works even if bfcLoc is NULL.

#49 csoneson closed 3 years ago
3
Error with 'download.file' on Linux cluster

#48 lmweber closed 3 years ago
2
Bioconda version still 1.6.2

#47 matmu closed 3 years ago
3
tximeta couldn't find matching transcriptome, returning non-ranged SummarizedExperiment

#46 matmu closed 3 years ago
2
batch processing compatibility

#45 stolarczyk closed 3 years ago
3
Extrating/adding gene_name to transcript level data

#44 kvittingseerup closed 3 years ago
5
Is it possible to extract transcript nucleotide sequence?

#43 kvittingseerup closed 3 years ago
5
Request: addCDS() function

#42 kvittingseerup closed 3 years ago
6
Tximeta, Salmon, and imported TPM

#41 FrAoJm closed 3 years ago
5
Check if GENCODE TxDb exists in AnnotationHub

#40 mikelove closed 3 years ago
3
Add support for new RefSeq seqlevelsStyle functionality

#39 mikelove opened 4 years ago
0
tximeta "couldn't find matching transcriptome, returning un-ranged SummarizedExperiment"

#38 mikelove opened 4 years ago
27
tximeta couldn't find matching transcriptome, returning non-ranged SummarizedExperiment

#37 AdeleMangelinck closed 4 years ago
8
Error in splitSE

#36 cnk113 closed 4 years ago
1
couldn't find matching transcriptome, returning un-ranged SummarizedExperiment

#35 sunliang3361 closed 4 years ago
4
Error: couldn't find matching transcriptome when using Salmon Mouse index from Ensembl

#34 diegoalzatec86 closed 4 years ago
6
Issue with finding matching exome/makeLinkedTxome

#33 malawsky closed 4 years ago
4
Customized import of alevin bootstrap counts

#32 k3yavi closed 4 years ago
1