jorainer ensembldb issues

jorainer / ensembldb

This is the ensembldb development repository.

https://jorainer.github.io/ensembldb

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issues

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The output from proteinToGenome has empty value

#157 zyh4482 opened 2 weeks ago
0
I found a terrorible mistake... `genome_build: GRCh37` for v112 and `genome_build: GRCh38` for v111.

#156 zyh4482 closed 2 weeks ago
1
missing data in human EnsDb v112?

#155 guidohooiveld opened 3 weeks ago
13
How to create edb from GTF and add protein data?

#154 zyh4482 closed 3 weeks ago
8
Trying to install ensembldb in Rstudio 3.6.3

#153 noodlebasket1 opened 1 month ago
2
Can we use ensembldb to convert transcriptomic bam to genomic bam?

#152 smk5g5 opened 3 months ago
1
AminoAcid to Genome Coordinates

#151 chhorstmann opened 3 months ago
1
support for parallel by preloading data

#150 Tim-Yu closed 7 months ago
0
Support for parallel query for coordinates mappings

#149 Tim-Yu closed 7 months ago
1
genomeToTranscript not mapping certain ranges (including entire chromosomes)

#148 cjagla closed 10 months ago
2
multiple EnsDb for mouse @ AnnotationHub: which one to use?

#147 guidohooiveld closed 1 year ago
3
Error getting gene regions from Homo.sapiens

#146 lmckinno opened 1 year ago
3
EnsDb for Ovis aries

#145 prispi86 closed 1 year ago
5
org.Ss.eg.db or Atlantic salmon database?

#144 marwa38 opened 1 year ago
1
`ensembldb` failing on Bioc devel (3.17)

#143 bschilder closed 1 year ago
3
replace disjointExons by exonicParts

#142 jorainer opened 1 year ago
0
spell

#141 mikelove closed 1 year ago
0
Turn regular function proteinToGenome() into S4 method

#140 hpages closed 1 year ago
0
Retrieving older annotations while matching API version

#139 rcastelo opened 1 year ago
14
refactor: don't report duplicated tx_id columns (issue #136)

#138 jorainer closed 2 years ago
0
genomeToProtein doesn't match protein if input CDS range contains a stop codon

#137 kotliary opened 2 years ago
4
genomeToProtein's output contains metadata with two identical tx_id columns

#136 kotliary closed 2 years ago
1
ensembldb and dplyr: filter, select

#135 Shicheng-Guo opened 2 years ago
5
Unable to retrieve sequence lengths from Ensembl

#134 tomthun opened 2 years ago
1
Mitochondrial chromosome is circular but isCircular(edb)["MT"] value is set as FALSE in the ensembldb object

#133 manogenome closed 2 years ago
8
getGeneRegionTrackForGviz -- syntax error

#132 plger closed 2 years ago
9
Fix link to ensembldb vignette source

#131 lgatto closed 2 years ago
0
Can not get the sequence lengths from Ensembl or Ensemblgenomes.

#130 qingzengLi closed 2 years ago
0
Argument "-P" isn't numeric

#129 guidohooiveld opened 2 years ago
2
Warning: Columns 'name', 'value' are not present in the database and have been removed

#128 lgatto opened 2 years ago
6
fix: all_ok check for empyt GRangesList (see issue #126)

#127 lgatto closed 2 years ago
3
Error in normalizeDoubleBracketSubscript(i, x, exact = exact, allow.NA = TRUE, : subscript is out of bounds

#126 lgatto closed 2 years ago
6
Add parameter to ensure mapping is only performed on canonical transcript

#125 jorainer opened 2 years ago
1
Installing error on Mac

#124 Pedramto89 opened 2 years ago
10
Coordinate retrieval errors on peptide belonging to multiple transcripts

#123 manogenome opened 2 years ago
13
Restore backward compatibility

#122 jorainer closed 2 years ago
1
Extract transcript name from Gtf/Ensembl

#121 jorainer closed 2 years ago
19
Older Version of Ensembldb with R > 4.0

#120 rbenel closed 2 years ago
2
proteinToTranscript not working for leaderless transcripts

#119 elstondsouza closed 2 years ago
4
Ensembl release 104

#118 guidohooiveld closed 2 years ago
6
ensDbFromGtf does not read uncompressed files: Error in UseMethod("close")

#117 egaffo closed 3 years ago
3
function to retrieve chr_pos_ref_alt by rs ID?

#116 Shicheng-Guo opened 3 years ago
1
Need for the filter on Tags (TSL:1, MANE Select etc.)

#115 Tim-Yu closed 2 years ago
8
GFF parser isn't detecting `gff-version` directive correctly

#114 mjsteinbaugh closed 3 years ago
4
Suppressing unwanted warnings during `ensDbFromGtf()` call

#113 mjsteinbaugh closed 3 years ago
3
ah <- AnnotationHub() ---error---- `filter_()` is deprecated as of dplyr 0.7.0

#112 CQgit closed 3 years ago
0
R suspend when loading ensembldb or annotation package based on ensembldb

#111 Yunuuuu closed 3 years ago
3
Cant retrieve reference information

#110 danielcgingerich opened 3 years ago
1
Filter by CANONICAL transcript

#109 pantastheo closed 3 years ago
7
How to specify the version of Ensembl Genomes not the main Ensembl database

#108 altairwei closed 3 years ago
2