Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / ropensci/biomartr issues and pull requests
#109 - Bacteria collection corner case bug fixed, Ready for push to CRAN
Pull Request -
State: closed - Opened by Roleren 10 months ago
- 1 comment
#108 - Generalized biomart database interface
Pull Request -
State: closed - Opened by Roleren 10 months ago
- 1 comment
#107 - `listGenomes()` fails to filter by *subset* with Ensembl Genomes instances
Issue -
State: closed - Opened by almeidasilvaf 11 months ago
- 3 comments
#106 - Fixed bug for ensembl ftp base url path for windows
Pull Request -
State: closed - Opened by Roleren 11 months ago
- 1 comment
#105 - skip_bacteria = FALSE resulting in unexpected behavior in is.genome.available()
Issue -
State: closed - Opened by JPReceveur 12 months ago
- 2 comments
Labels: bug
#104 - Generalized getCollection with support for biomartr:::supported_biotypes. Also tests now run 2x faster.
Pull Request -
State: closed - Opened by Roleren 12 months ago
- 3 comments
#103 - Fixed uniprot fetch, more tests and improved gencode assembly accession selector
Pull Request -
State: closed - Opened by Roleren 12 months ago
- 11 comments
#102 - Generalization of the whole sequence and annotation part of package is done
Pull Request -
State: closed - Opened by Roleren about 1 year ago
#101 - Fixing proteom for ensembl genomes species, issue 84
Pull Request -
State: closed - Opened by Roleren about 1 year ago
#100 - Massive update of generalized code and improvements
Pull Request -
State: closed - Opened by Roleren about 1 year ago
- 5 comments
#99 - Fixed new rest API url and simplified functions to be more generalized
Pull Request -
State: closed - Opened by Roleren about 1 year ago
- 1 comment
#98 - Fixed API call change from ensembl side to work now, also simplified …
Pull Request -
State: closed - Opened by Roleren about 1 year ago
#97 - Error retrieving non-human genomes from ensembl
Issue -
State: closed - Opened by cjagla about 1 year ago
- 5 comments
#96 - Small fix for bacterial collections
Pull Request -
State: closed - Opened by Roleren about 1 year ago
- 1 comment
#95 - Possible Ensembl SSL connectivity problems detected.
Issue -
State: closed - Opened by pyrevo about 1 year ago
- 10 comments
#94 - Major revision for bug fixes and generalization of whole package
Pull Request -
State: closed - Opened by Roleren about 1 year ago
- 1 comment
#93 - getGenomeSet() Error
Issue -
State: closed - Opened by pfresia over 1 year ago
- 1 comment
#92 - Error in `dplyr::bind_rows()`: ! Can't combine `..1$X35` <double> and `..9$X35` <character>.
Issue -
State: closed - Opened by HajkD over 1 year ago
- 1 comment
#91 - specific genes/features from list of refseqs
Issue -
State: closed - Opened by omarkr8 over 1 year ago
- 4 comments
#90 - Assembly summary txt download failed; Something went wrong when trying to access the FTP site
Issue -
State: closed - Opened by xl0418 over 1 year ago
- 2 comments
#89 - Bump version
Pull Request -
State: closed - Opened by Roleren over 1 year ago
#88 - https and new curl fix
Pull Request -
State: closed - Opened by Roleren almost 2 years ago
- 1 comment
#87 - getENSEMBL.Seq: Found organism but given release number did not specify existing file in ensembl...
Issue -
State: closed - Opened by ibphuangchen almost 2 years ago
- 2 comments
#86 - Downloads not working; setup on windows?
Issue -
State: closed - Opened by raydioactive almost 2 years ago
- 4 comments
#85 - Retrieve genes from a locus by knowing the chromosome position
Issue -
State: closed - Opened by zh-zhang1984 almost 2 years ago
- 1 comment
#84 - Listing and downloading all proteomes from Ensembl Plants/Fungi/Protists
Issue -
State: closed - Opened by almeidasilvaf about 2 years ago
- 3 comments
#83 - Download of genomes fails when release number and/or assembly type are provided
Issue -
State: closed - Opened by vizkidd about 2 years ago
- 5 comments
#82 - Uniprot FASTA database download failed
Issue -
State: closed - Opened by wardiam about 2 years ago
- 4 comments
#81 - Refseq download failure for Windows
Issue -
State: closed - Opened by jarditi0011 about 2 years ago
- 3 comments
#80 - Lock error in 4.1.1 not in 4.03
Issue -
State: closed - Opened by ZheFrench over 2 years ago
- 2 comments
#79 - fix badge paragraph for detection by pkgdown
Pull Request -
State: closed - Opened by maelle almost 3 years ago
#78 - Fix title in NEWS.md
Pull Request -
State: closed - Opened by maelle almost 3 years ago
- 1 comment
#77 - Error during genome retrieval
Issue -
State: closed - Opened by Ste40cm almost 3 years ago
- 3 comments
#76 - refseq download error
Issue -
State: closed - Opened by cmatKhan almost 3 years ago
- 6 comments
#75 - R session aborted in downloading process
Issue -
State: closed - Opened by jimrpy almost 3 years ago
- 8 comments
#74 - errors in getGO
Issue -
State: closed - Opened by rocpengliu over 3 years ago
- 2 comments
#73 - meta.retrieval error "Argument 1 must have names"
Issue -
State: closed - Opened by dominikmerges over 3 years ago
- 5 comments
#72 - meta.retrieval fails with NA/NA_assembly_stats.txt
Issue -
State: closed - Opened by dominikmerges over 3 years ago
- 8 comments
#71 - Using taxid for genome retrieval does not work for any species or strain
Issue -
State: closed - Opened by raphaelajoos over 3 years ago
- 3 comments
#70 - Inconclusive results with is.genome.available()
Issue -
State: closed - Opened by johanneswerner over 3 years ago
- 3 comments
#69 - Performance issue
Issue -
State: closed - Opened by johanneswerner over 3 years ago
- 7 comments
#68 - How to download all genomes that belong to a specific taxa?
Issue -
State: open - Opened by johanneswerner over 3 years ago
- 8 comments
Labels: enhancement, help wanted
#67 - Small bug fix of ssl in linux
Issue -
State: closed - Opened by Roleren almost 4 years ago
- 1 comment
#66 - fixed new ssl bug for linux 20.04
Pull Request -
State: closed - Opened by Roleren almost 4 years ago
- 1 comment
#65 - Can I download proteomes of upper taxonomic levels?
Issue -
State: closed - Opened by iquasere almost 4 years ago
- 4 comments
#64 - there is no package called ‘biomartr’
Issue -
State: closed - Opened by iquasere almost 4 years ago
- 2 comments
#63 - Unable to download SARS genomes
Issue -
State: closed - Opened by mariaasierra almost 4 years ago
- 1 comment
#62 - one same ensembl ID gets multiple entrez IDs with same gene symbol
Issue -
State: closed - Opened by amssljc almost 4 years ago
- 1 comment
#61 - Fixed download of earlier release ensembl genomes
Pull Request -
State: closed - Opened by Roleren almost 4 years ago
- 3 comments
#60 - curl handshake failure, Ubuntu 20.04
Issue -
State: closed - Opened by Roleren almost 4 years ago
- 2 comments
#59 - Unable to connect to server
Issue -
State: closed - Opened by limfs92 about 4 years ago
- 2 comments
#58 - Download sequences by id
Issue -
State: closed - Opened by missuse about 4 years ago
- 5 comments
Labels: enhancement
#57 - read_cds fails when returning in data.table format
Issue -
State: closed - Opened by clementfkent about 4 years ago
- 4 comments
#56 - Assembly type argument implementation
Pull Request -
State: closed - Opened by Roleren about 4 years ago
- 7 comments
#55 - Ensembl primary assembly
Issue -
State: closed - Opened by Roleren over 4 years ago
- 7 comments
#54 - how to download all bacterial genomes from specific phylum
Issue -
State: closed - Opened by javadgh6 over 4 years ago
- 3 comments
#53 - Checking existence of specific genome in getCollection function
Issue -
State: closed - Opened by TakahiroYamada over 4 years ago
- 2 comments
#52 - getProteomeSet silently downloads wrong fasta file
Issue -
State: closed - Opened by AlexNesm over 4 years ago
- 2 comments
#51 - server certificate verification failed
Issue -
State: closed - Opened by 276562578 over 4 years ago
- 5 comments
#50 - Point to "assembly_summary.txt" instead of downloading files
Issue -
State: closed - Opened by taylorreiter over 4 years ago
- 7 comments
Labels: enhancement
#49 - Homo sapiens rsid to geneid
Issue -
State: closed - Opened by kokyriakidis over 4 years ago
- 1 comment
#48 - Download Genbank all fungi genomes and genes
Issue -
State: closed - Opened by liuxianghui over 4 years ago
- 1 comment
#47 - Question about downloading mitochondrial genomes
Issue -
State: open - Opened by ucbtmae almost 5 years ago
- 3 comments
Labels: enhancement, help wanted
#46 - getRNA followed read_rna with wrong data type
Issue -
State: closed - Opened by AlexanderBartholomaeus about 5 years ago
- 3 comments
#45 - How to download GRCh37 data?
Issue -
State: closed - Opened by ShixiangWang about 5 years ago
- 10 comments
#44 - Amount of data accessed with biomartr?
Issue -
State: closed - Opened by sckott about 5 years ago
- 4 comments
#43 - the library cannot properly handle "Heterocephalus glaber female"
Issue -
State: closed - Opened by antonkulaga about 5 years ago
- 3 comments
#42 - Could not retrieve Encode regions
Issue -
State: closed - Opened by tayaza about 5 years ago
- 1 comment
#41 - Could not retrieve Encode regions
Issue -
State: closed - Opened by tayaza about 5 years ago
- 4 comments
#40 - High RAM usage when using meta.retrieval prevents usage on low end machines
Issue -
State: open - Opened by barrel0luck over 5 years ago
- 4 comments
Labels: enhancement, help wanted
#39 - Error when downloading multiple CDS files (not meta.retrieval)
Issue -
State: closed - Opened by eggrandio over 5 years ago
- 2 comments
#38 - Error on the md5 hash check step
Issue -
State: closed - Opened by philippmuench over 5 years ago
- 7 comments
#37 - EnsemblBacteria: Error: '/tmp/RtmppaSXUW/EnsemblBacteria.txt' does not exist.
Issue -
State: closed - Opened by ndaniel over 5 years ago
- 5 comments
#36 - Immediate problem on install - getMarts crashing
Issue -
State: closed - Opened by aleighbrown over 5 years ago
- 3 comments
#35 - Error in curl::curl_fetch_memory("www.google.com")
Issue -
State: closed - Opened by SepOrion almost 6 years ago
- 6 comments
#34 - Error in downloading bacterial group
Issue -
State: closed - Opened by mehmetdirenc almost 6 years ago
- 7 comments
#33 - Use stringr::str_to_title() for Ensembl filenames
Pull Request -
State: closed - Opened by milescsmith about 6 years ago
- 1 comment
#32 - Adding a section "similar work" to README
Issue -
State: closed - Opened by sinarueeger about 6 years ago
- 4 comments
#31 - Specify Ensembl Plant version
Issue -
State: closed - Opened by timedreamer about 6 years ago
- 5 comments
#30 - get groups() doesn't provide information for database ensemblgenomes
Issue -
State: closed - Opened by anilsakshi about 6 years ago
- 1 comment
#29 - getGenome function not working for viruses?
Issue -
State: closed - Opened by pedur1 over 6 years ago
- 1 comment
Labels: bug
#28 - Issue after Recovering
Issue -
State: closed - Opened by 3719left over 6 years ago
- 8 comments
Labels: bug
#27 - ftp issues when using meta.retrieval
Issue -
State: closed - Opened by seannamctaggart over 6 years ago
- 9 comments
#26 - this slack notification token will actually work
Pull Request -
State: closed - Opened by sckott over 6 years ago
#25 - GO term missing for my specie (prunus persica) on EnsemblPlants Biomart
Issue -
State: closed - Opened by pjmartinez over 6 years ago
- 1 comment
#24 - adds ropensci slack notification (with encrypted token) to travis file
Pull Request -
State: closed - Opened by sckott over 6 years ago
#23 - getGO exclude cellular component and take from level 3 onwards
Issue -
State: closed - Opened by mominchen over 6 years ago
#22 - Support genome retrieval for misclassified species
Issue -
State: closed - Opened by lutteropp almost 7 years ago
- 3 comments
Labels: enhancement, help wanted
#21 - Support species synonyms
Issue -
State: open - Opened by lutteropp almost 7 years ago
- 2 comments
Labels: enhancement, help wanted
#20 - Some genomes are not found despite them being in the database
Issue -
State: closed - Opened by lutteropp almost 7 years ago
- 1 comment
#19 - modified DESCRIPTION, and added codemeta.json
Pull Request -
State: closed - Opened by chrisfan24 almost 7 years ago
#18 - requesting some info for JSON-LD metadata
Issue -
State: closed - Opened by chrisfan24 almost 7 years ago
- 1 comment
#17 - Please use git tags and releases
Issue -
State: closed - Opened by sckott about 7 years ago
- 5 comments
#16 - Example of csv file for biomatr
Issue -
State: closed - Opened by NasDenis about 7 years ago
- 7 comments
#15 - Added rOpenSci review badge
Pull Request -
State: closed - Opened by karthik about 7 years ago
#14 - Question about mapping SNPs to Genes with biomartR
Issue -
State: closed - Opened by arbet003 about 7 years ago
- 1 comment
#13 - Retrieval of different ENSEMBL and NCBI versions
Issue -
State: closed - Opened by HajkD over 7 years ago
- 2 comments
Labels: enhancement
#12 - ftp errors when using meta.retrieval
Issue -
State: closed - Opened by NicoleGruenheit over 7 years ago
- 4 comments
Labels: enhancement
#11 - Question: BiomaRt?
Issue -
State: closed - Opened by zx8754 over 7 years ago
- 1 comment
Labels: question
#10 - Extend listGenomes() output
Issue -
State: open - Opened by HajkD over 7 years ago
Labels: enhancement, help wanted