Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / jorainer/ensembldb issues and pull requests
#159 - Compatibility between `EnsDb` objects and `BSgenome` objects
Issue -
State: open - Opened by mschubert about 2 months ago
- 1 comment
#158 - AnnotationHub EnsDb object for GRCh37?
Issue -
State: open - Opened by mschubert about 2 months ago
- 1 comment
#157 - The output from proteinToGenome has empty value
Issue -
State: closed - Opened by zyh4482 4 months ago
- 6 comments
#156 - I found a terrorible mistake... `genome_build: GRCh37` for v112 and `genome_build: GRCh38` for v111.
Issue -
State: closed - Opened by zyh4482 4 months ago
- 1 comment
#155 - missing data in human EnsDb v112?
Issue -
State: open - Opened by guidohooiveld 4 months ago
- 14 comments
#154 - How to create edb from GTF and add protein data?
Issue -
State: closed - Opened by zyh4482 4 months ago
- 8 comments
#153 - Trying to install ensembldb in Rstudio 3.6.3
Issue -
State: open - Opened by noodlebasket1 5 months ago
- 2 comments
#152 - Can we use ensembldb to convert transcriptomic bam to genomic bam?
Issue -
State: open - Opened by smk5g5 6 months ago
- 1 comment
#151 - AminoAcid to Genome Coordinates
Issue -
State: open - Opened by chhorstmann 7 months ago
- 1 comment
#150 - support for parallel by preloading data
Pull Request -
State: closed - Opened by Tim-Yu 11 months ago
#149 - Support for parallel query for coordinates mappings
Issue -
State: closed - Opened by Tim-Yu 12 months ago
- 1 comment
#148 - genomeToTranscript not mapping certain ranges (including entire chromosomes)
Issue -
State: closed - Opened by cjagla about 1 year ago
- 2 comments
#147 - multiple EnsDb for mouse @ AnnotationHub: which one to use?
Issue -
State: closed - Opened by guidohooiveld over 1 year ago
- 3 comments
#146 - Error getting gene regions from Homo.sapiens
Issue -
State: open - Opened by lmckinno over 1 year ago
- 3 comments
#145 - EnsDb for Ovis aries
Issue -
State: closed - Opened by prispi86 over 1 year ago
- 5 comments
#144 - org.Ss.eg.db or Atlantic salmon database?
Issue -
State: open - Opened by marwa38 almost 2 years ago
- 1 comment
#143 - `ensembldb` failing on Bioc devel (3.17)
Issue -
State: closed - Opened by bschilder almost 2 years ago
- 3 comments
#142 - replace disjointExons by exonicParts
Issue -
State: open - Opened by jorainer almost 2 years ago
#141 - spell
Pull Request -
State: closed - Opened by mikelove about 2 years ago
#140 - Turn regular function proteinToGenome() into S4 method
Pull Request -
State: closed - Opened by hpages about 2 years ago
#139 - Retrieving older annotations while matching API version
Issue -
State: open - Opened by rcastelo about 2 years ago
- 14 comments
#138 - refactor: don't report duplicated tx_id columns (issue #136)
Pull Request -
State: closed - Opened by jorainer over 2 years ago
#137 - genomeToProtein doesn't match protein if input CDS range contains a stop codon
Issue -
State: open - Opened by kotliary over 2 years ago
- 4 comments
#136 - genomeToProtein's output contains metadata with two identical tx_id columns
Issue -
State: closed - Opened by kotliary over 2 years ago
- 1 comment
#135 - ensembldb and dplyr: filter, select
Issue -
State: open - Opened by Shicheng-Guo over 2 years ago
- 7 comments
#134 - Unable to retrieve sequence lengths from Ensembl
Issue -
State: open - Opened by tomthun over 2 years ago
- 1 comment
#133 - Mitochondrial chromosome is circular but isCircular(edb)["MT"] value is set as FALSE in the ensembldb object
Issue -
State: closed - Opened by manogenome over 2 years ago
- 8 comments
#132 - getGeneRegionTrackForGviz -- syntax error
Issue -
State: closed - Opened by plger over 2 years ago
- 9 comments
#131 - Fix link to ensembldb vignette source
Pull Request -
State: closed - Opened by lgatto over 2 years ago
#130 - Can not get the sequence lengths from Ensembl or Ensemblgenomes.
Issue -
State: closed - Opened by qingzengLi over 2 years ago
#129 - Argument "-P" isn't numeric
Issue -
State: open - Opened by guidohooiveld over 2 years ago
- 2 comments
#128 - Warning: Columns 'name', 'value' are not present in the database and have been removed
Issue -
State: open - Opened by lgatto over 2 years ago
- 6 comments
#127 - fix: all_ok check for empyt GRangesList (see issue #126)
Pull Request -
State: closed - Opened by lgatto almost 3 years ago
- 3 comments
#126 - Error in normalizeDoubleBracketSubscript(i, x, exact = exact, allow.NA = TRUE, : subscript is out of bounds
Issue -
State: closed - Opened by lgatto almost 3 years ago
- 6 comments
#125 - Add parameter to ensure mapping is only performed on canonical transcript
Issue -
State: open - Opened by jorainer almost 3 years ago
- 1 comment
#124 - Installing error on Mac
Issue -
State: open - Opened by Pedramto89 almost 3 years ago
- 10 comments
#123 - Coordinate retrieval errors on peptide belonging to multiple transcripts
Issue -
State: open - Opened by manogenome almost 3 years ago
- 13 comments
#122 - Restore backward compatibility
Issue -
State: closed - Opened by jorainer almost 3 years ago
- 1 comment
#121 - Extract transcript name from Gtf/Ensembl
Issue -
State: closed - Opened by jorainer almost 3 years ago
- 19 comments
#120 - Older Version of Ensembldb with R > 4.0
Issue -
State: closed - Opened by rbenel about 3 years ago
- 2 comments
#119 - proteinToTranscript not working for leaderless transcripts
Issue -
State: closed - Opened by elstondsouza about 3 years ago
- 4 comments
#118 - Ensembl release 104
Issue -
State: closed - Opened by guidohooiveld about 3 years ago
- 6 comments
#117 - ensDbFromGtf does not read uncompressed files: Error in UseMethod("close")
Issue -
State: closed - Opened by egaffo over 3 years ago
- 3 comments
#116 - function to retrieve chr_pos_ref_alt by rs ID?
Issue -
State: open - Opened by Shicheng-Guo over 3 years ago
- 1 comment
#115 - Need for the filter on Tags (TSL:1, MANE Select etc.)
Issue -
State: closed - Opened by Tim-Yu over 3 years ago
- 8 comments
#114 - GFF parser isn't detecting `gff-version` directive correctly
Issue -
State: closed - Opened by mjsteinbaugh over 3 years ago
- 4 comments
#113 - Suppressing unwanted warnings during `ensDbFromGtf()` call
Issue -
State: closed - Opened by mjsteinbaugh over 3 years ago
- 3 comments
#112 - ah <- AnnotationHub() ---error---- `filter_()` is deprecated as of dplyr 0.7.0
Issue -
State: closed - Opened by CQgit over 3 years ago
#111 - R suspend when loading ensembldb or annotation package based on ensembldb
Issue -
State: closed - Opened by Yunuuuu almost 4 years ago
- 3 comments
#110 - Cant retrieve reference information
Issue -
State: open - Opened by danielcgingerich almost 4 years ago
- 1 comment
#109 - Filter by CANONICAL transcript
Issue -
State: closed - Opened by pantastheo almost 4 years ago
- 7 comments
Labels: enhancement
#108 - How to specify the version of Ensembl Genomes not the main Ensembl database
Issue -
State: closed - Opened by altairwei about 4 years ago
- 2 comments
#107 - using EnsDb on sqlite file crash further RMariaDB connections
Issue -
State: open - Opened by kforner about 4 years ago
- 3 comments
#106 - No CDS found (proteinToGenome)
Issue -
State: open - Opened by Zupanova about 4 years ago
- 5 comments
#105 - Cannot find function transcriptToGenome
Issue -
State: closed - Opened by ahdee almost 5 years ago
- 2 comments
#104 - mapIds() should fail when keys are invalid
Issue -
State: closed - Opened by mtmorgan almost 5 years ago
- 3 comments
#103 - Inclusion of GC content?
Issue -
State: closed - Opened by smped almost 5 years ago
- 6 comments
#102 - getting the mouse transcript sequence by ensembldb
Issue -
State: closed - Opened by Ci-TJ about 5 years ago
- 10 comments
#100 - mapIds(..., multiVal="asNA") returns logical() instead of character() when all ids map multiply
Issue -
State: open - Opened by mtmorgan about 5 years ago
- 6 comments
#99 - Build a human hg38 EnsDb of an older Ensembl release (v79)
Issue -
State: closed - Opened by ccwang002 over 5 years ago
- 3 comments
#98 - Building the DB from prefetched txt files
Issue -
State: open - Opened by harish0201 over 5 years ago
- 5 comments
#97 - Problem with ensDbFromGff using recent ensembl gff files
Issue -
State: open - Opened by stephenrong over 5 years ago
- 17 comments
#96 - Just a test - delete me
Issue -
State: closed - Opened by ghost over 5 years ago
#95 - Switch from FaFiles to TwobitFiles
Issue -
State: closed - Opened by jorainer over 5 years ago
#94 - Add intronsByTranscript method
Issue -
State: closed - Opened by jorainer over 5 years ago
#93 - Error when converting from genomic to transcriptomic coordinates
Issue -
State: closed - Opened by marcasriv over 5 years ago
- 4 comments
Labels: bug
#92 - Improve performance of mapping functions
Issue -
State: closed - Opened by jorainer over 5 years ago
- 7 comments
#91 - compare mapping functions with GenomicFeatures::mapFromTranscripts
Issue -
State: closed - Opened by jorainer over 5 years ago
- 2 comments
#90 - Discrepancy between UCSC/NCBI and ensembldb in genome to transcript mapping
Issue -
State: closed - Opened by jorainer almost 6 years ago
- 1 comment
#89 - Include transcript/protein version in the database
Issue -
State: closed - Opened by ccwang002 almost 6 years ago
- 8 comments
#88 - Provide mapping of non standard chromosome names from ensembl to UCSC
Issue -
State: open - Opened by ivanek almost 6 years ago
- 6 comments
#87 - implement mapIds(multiVals = "CharacterList")
Pull Request -
State: closed - Opened by mtmorgan almost 6 years ago
- 2 comments
#86 - Not picking up circular DNA correctly
Issue -
State: open - Opened by jorainer almost 6 years ago
- 3 comments
#85 - transcriptToGenome problem
Issue -
State: closed - Opened by smaegol almost 6 years ago
- 4 comments
#84 - local MySQL installation error
Issue -
State: closed - Opened by shwong-tw almost 6 years ago
- 6 comments
#83 - Improve MySQL performance
Issue -
State: closed - Opened by jorainer about 6 years ago
#82 - Switch from RMySQL to RMariaDB
Issue -
State: closed - Opened by jorainer about 6 years ago
#81 - genomeToTranscript function not found
Issue -
State: closed - Opened by pamelarussell about 6 years ago
- 2 comments
#80 - Get the amoniacid name for each positition
Issue -
State: closed - Opened by Tato14 over 6 years ago
- 5 comments
#79 - Fix Rd warnings on Windows build machine
Issue -
State: closed - Opened by jorainer over 6 years ago
#78 - Add a filter for the protein_domain_source
Issue -
State: closed - Opened by jorainer over 6 years ago
#77 - Add mapping of transcripts to NCBI RefSeq
Issue -
State: open - Opened by jorainer over 6 years ago
- 6 comments
#76 - fix for issue #75
Pull Request -
State: closed - Opened by plijnzaad over 6 years ago
- 1 comment
#75 - ensDbFromGtf refuses to parse GTF file
Issue -
State: closed - Opened by plijnzaad over 6 years ago
- 7 comments
#74 - Unit test failure in extractTranscriptSeqs
Issue -
State: closed - Opened by jorainer over 6 years ago
- 1 comment
#73 - Implement a function to map from cds-relative to tx-relative coordinates
Issue -
State: closed - Opened by jorainer over 6 years ago
- 2 comments
#72 - Error creating EnsDb from Mmusculus v67 GTF
Issue -
State: closed - Opened by jorainer over 6 years ago
- 1 comment
#71 - Get the Swissprot IDs
Issue -
State: closed - Opened by jorainer almost 7 years ago
- 4 comments
#70 - Rsamtools does no longer export method path
Issue -
State: closed - Opened by jorainer almost 7 years ago
#69 - Some Granges with genomeToProtein: "Error: subscript contains NAs"
Issue -
State: closed - Opened by ibwoo almost 7 years ago
- 3 comments
#68 - Report mapped genomic coordinates in HGVS notation
Issue -
State: open - Opened by jorainer almost 7 years ago
#67 - genomeToProtein not working on GRanges object with >1 range
Issue -
State: closed - Opened by ibwoo almost 7 years ago
- 4 comments
#66 - heavyweight dependencies
Issue -
State: closed - Opened by lawremi almost 7 years ago
- 5 comments
#65 - Add/fix the proteinToGenome function
Issue -
State: closed - Opened by jorainer almost 7 years ago
#64 - Add transcriptToGenome function
Issue -
State: closed - Opened by jorainer almost 7 years ago
- 1 comment
#63 - Missing GenomeInfoDbData
Issue -
State: closed - Opened by mjsteinbaugh almost 7 years ago
- 5 comments
#62 - Update the coordinate-mapping vignette
Issue -
State: closed - Opened by jorainer almost 7 years ago
#61 - Add a genomeToTranscript function
Issue -
State: closed - Opened by jorainer almost 7 years ago
- 1 comment
#60 - Add a transcriptToGenome function
Issue -
State: closed - Opened by jorainer almost 7 years ago
- 1 comment