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

#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

#103 - Fixed uniprot fetch, more tests and improved gencode assembly accession selector

Pull Request - State: closed - Opened by Roleren 12 months ago - 11 comments

#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

#91 - specific genes/features from list of refseqs

Issue - State: closed - Opened by omarkr8 over 1 year ago - 4 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

#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

#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