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

#157 - The output from proteinToGenome has empty value

Issue - State: open - Opened by zyh4482 18 days ago

#155 - missing data in human EnsDb v112?

Issue - State: open - Opened by guidohooiveld 21 days ago - 11 comments

#154 - How to create edb from GTF and add protein data?

Issue - State: closed - Opened by zyh4482 about 1 month ago - 8 comments

#153 - Trying to install ensembldb in Rstudio 3.6.3

Issue - State: open - Opened by noodlebasket1 about 2 months ago - 2 comments

#152 - Can we use ensembldb to convert transcriptomic bam to genomic bam?

Issue - State: open - Opened by smk5g5 3 months ago - 1 comment

#151 - AminoAcid to Genome Coordinates

Issue - State: open - Opened by chhorstmann 4 months ago - 1 comment

#150 - support for parallel by preloading data

Pull Request - State: closed - Opened by Tim-Yu 8 months ago

#149 - Support for parallel query for coordinates mappings

Issue - State: closed - Opened by Tim-Yu 9 months ago - 1 comment

#148 - genomeToTranscript not mapping certain ranges (including entire chromosomes)

Issue - State: closed - Opened by cjagla 10 months ago - 2 comments

#147 - multiple EnsDb for mouse @ AnnotationHub: which one to use?

Issue - State: closed - Opened by guidohooiveld about 1 year ago - 3 comments

#146 - Error getting gene regions from Homo.sapiens

Issue - State: open - Opened by lmckinno about 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 over 1 year ago - 1 comment

#143 - `ensembldb` failing on Bioc devel (3.17)

Issue - State: closed - Opened by bschilder over 1 year ago - 3 comments

#142 - replace disjointExons by exonicParts

Issue - State: open - Opened by jorainer over 1 year ago

#141 - spell

Pull Request - State: closed - Opened by mikelove almost 2 years ago

#140 - Turn regular function proteinToGenome() into S4 method

Pull Request - State: closed - Opened by hpages almost 2 years ago

#139 - Retrieving older annotations while matching API version

Issue - State: open - Opened by rcastelo almost 2 years ago - 14 comments

#138 - refactor: don't report duplicated tx_id columns (issue #136)

Pull Request - State: closed - Opened by jorainer about 2 years ago

#137 - genomeToProtein doesn't match protein if input CDS range contains a stop codon

Issue - State: open - Opened by kotliary about 2 years ago - 4 comments

#136 - genomeToProtein's output contains metadata with two identical tx_id columns

Issue - State: closed - Opened by kotliary about 2 years ago - 1 comment

#135 - ensembldb and dplyr: filter, select

Issue - State: open - Opened by Shicheng-Guo about 2 years ago - 5 comments

#134 - Unable to retrieve sequence lengths from Ensembl

Issue - State: open - Opened by tomthun about 2 years ago - 1 comment

#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

#129 - Argument "-P" isn't numeric

Issue - State: open - Opened by guidohooiveld over 2 years ago - 2 comments

#127 - fix: all_ok check for empyt GRangesList (see issue #126)

Pull Request - State: closed - Opened by lgatto over 2 years ago - 3 comments

#125 - Add parameter to ensure mapping is only performed on canonical transcript

Issue - State: open - Opened by jorainer over 2 years ago - 1 comment

#124 - Installing error on Mac

Issue - State: open - Opened by Pedramto89 over 2 years ago - 10 comments

#123 - Coordinate retrieval errors on peptide belonging to multiple transcripts

Issue - State: open - Opened by manogenome over 2 years ago - 13 comments

#122 - Restore backward compatibility

Issue - State: closed - Opened by jorainer over 2 years ago - 1 comment

#121 - Extract transcript name from Gtf/Ensembl

Issue - State: closed - Opened by jorainer over 2 years ago - 19 comments

#120 - Older Version of Ensembldb with R > 4.0

Issue - State: closed - Opened by rbenel almost 3 years ago - 2 comments

#119 - proteinToTranscript not working for leaderless transcripts

Issue - State: closed - Opened by elstondsouza almost 3 years ago - 4 comments

#118 - Ensembl release 104

Issue - State: closed - Opened by guidohooiveld almost 3 years ago - 6 comments

#117 - ensDbFromGtf does not read uncompressed files: Error in UseMethod("close")

Issue - State: closed - Opened by egaffo about 3 years ago - 3 comments

#116 - function to retrieve chr_pos_ref_alt by rs ID?

Issue - State: open - Opened by Shicheng-Guo about 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

#111 - R suspend when loading ensembldb or annotation package based on ensembldb

Issue - State: closed - Opened by Yunuuuu over 3 years ago - 3 comments

#110 - Cant retrieve reference information

Issue - State: open - Opened by danielcgingerich over 3 years ago - 1 comment

#109 - Filter by CANONICAL transcript

Issue - State: closed - Opened by pantastheo over 3 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 almost 4 years ago - 2 comments

#107 - using EnsDb on sqlite file crash further RMariaDB connections

Issue - State: open - Opened by kforner almost 4 years ago - 3 comments

#106 - No CDS found (proteinToGenome)

Issue - State: open - Opened by Zupanova almost 4 years ago - 5 comments

#105 - Cannot find function transcriptToGenome

Issue - State: closed - Opened by ahdee over 4 years ago - 2 comments

#104 - mapIds() should fail when keys are invalid

Issue - State: closed - Opened by mtmorgan over 4 years ago - 3 comments

#103 - Inclusion of GC content?

Issue - State: closed - Opened by smped over 4 years ago - 6 comments

#102 - getting the mouse transcript sequence by ensembldb

Issue - State: closed - Opened by Ci-TJ almost 5 years ago - 10 comments

#101 - ..

Issue - State: closed - Opened by Ci-TJ almost 5 years ago

#99 - Build a human hg38 EnsDb of an older Ensembl release (v79)

Issue - State: closed - Opened by ccwang002 almost 5 years ago - 3 comments

#98 - Building the DB from prefetched txt files

Issue - State: open - Opened by harish0201 about 5 years ago - 5 comments

#97 - Problem with ensDbFromGff using recent ensembl gff files

Issue - State: open - Opened by stephenrong about 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 over 5 years ago - 1 comment

#89 - Include transcript/protein version in the database

Issue - State: closed - Opened by ccwang002 over 5 years ago - 8 comments

#88 - Provide mapping of non standard chromosome names from ensembl to UCSC

Issue - State: open - Opened by ivanek over 5 years ago - 6 comments

#87 - implement mapIds(multiVals = "CharacterList")

Pull Request - State: closed - Opened by mtmorgan over 5 years ago - 2 comments

#86 - Not picking up circular DNA correctly

Issue - State: open - Opened by jorainer over 5 years ago - 3 comments

#85 - transcriptToGenome problem

Issue - State: closed - Opened by smaegol over 5 years ago - 4 comments

#84 - local MySQL installation error

Issue - State: closed - Opened by shwong-tw over 5 years ago - 6 comments

#83 - Improve MySQL performance

Issue - State: closed - Opened by jorainer almost 6 years ago

#82 - Switch from RMySQL to RMariaDB

Issue - State: closed - Opened by jorainer almost 6 years ago

#81 - genomeToTranscript function not found

Issue - State: closed - Opened by pamelarussell almost 6 years ago - 2 comments

#80 - Get the amoniacid name for each positition

Issue - State: closed - Opened by Tato14 almost 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 over 6 years ago - 4 comments

#70 - Rsamtools does no longer export method path

Issue - State: closed - Opened by jorainer over 6 years ago

#69 - Some Granges with genomeToProtein: "Error: subscript contains NAs"

Issue - State: closed - Opened by ibwoo over 6 years ago - 3 comments

#68 - Report mapped genomic coordinates in HGVS notation

Issue - State: open - Opened by jorainer over 6 years ago

#67 - genomeToProtein not working on GRanges object with >1 range

Issue - State: closed - Opened by ibwoo over 6 years ago - 4 comments

#66 - heavyweight dependencies

Issue - State: closed - Opened by lawremi over 6 years ago - 5 comments

#65 - Add/fix the proteinToGenome function

Issue - State: closed - Opened by jorainer over 6 years ago

#64 - Add transcriptToGenome function

Issue - State: closed - Opened by jorainer over 6 years ago - 1 comment

#63 - Missing GenomeInfoDbData

Issue - State: closed - Opened by mjsteinbaugh over 6 years ago - 5 comments

#62 - Update the coordinate-mapping vignette

Issue - State: closed - Opened by jorainer over 6 years ago

#61 - Add a genomeToTranscript function

Issue - State: closed - Opened by jorainer over 6 years ago - 1 comment

#60 - Add a transcriptToGenome function

Issue - State: closed - Opened by jorainer over 6 years ago - 1 comment

#59 - Add a genomeToProtein function

Issue - State: closed - Opened by jorainer over 6 years ago

#58 - Add a proteinToTranscript function

Issue - State: closed - Opened by jorainer over 6 years ago - 2 comments