Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / drostlab/orthologr issues and pull requests

#48 - How to use Orthofinder2 as ortho_detection?

Issue - State: closed - Opened by ZexuanZhao about 1 year ago

#48 - How to use Orthofinder2 as ortho_detection?

Issue - State: closed - Opened by ZexuanZhao about 1 year ago

#47 - Add instructions for installing DIAMOND

Pull Request - State: closed - Opened by LotharukpongJS over 1 year ago

#47 - Add instructions for installing DIAMOND

Pull Request - State: closed - Opened by LotharukpongJS over 1 year ago

#46 - DIAMOND2 as the default sequence aligner.

Pull Request - State: closed - Opened by LotharukpongJS over 1 year ago - 1 comment

#46 - DIAMOND2 as the default sequence aligner.

Pull Request - State: closed - Opened by LotharukpongJS over 1 year ago - 1 comment

#45 - Dependency question

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

#45 - Dependency question

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

#44 - Updates to package description and news.

Pull Request - State: closed - Opened by LotharukpongJS over 1 year ago

#44 - Updates to package description and news.

Pull Request - State: closed - Opened by LotharukpongJS over 1 year ago

#43 - Package release request

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

#43 - Package release request

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

#42 - Docker image request

Issue - State: closed - Opened by gallardoalba over 1 year ago - 1 comment

#42 - Docker image request

Issue - State: closed - Opened by gallardoalba over 1 year ago - 1 comment

#41 - h(simpleErrpr(msg, call)) error

Issue - State: open - Opened by DanielleMStevens over 1 year ago - 4 comments

#41 - h(simpleErrpr(msg, call)) error

Issue - State: open - Opened by DanielleMStevens over 1 year ago - 4 comments

#40 - Issue running blastp in dnds

Issue - State: closed - Opened by jennifercalawa over 1 year ago - 2 comments

#40 - Issue running blastp in dnds

Issue - State: closed - Opened by jennifercalawa over 1 year ago - 2 comments

#39 - Minor changes to remove three warnings when running devtools::check()

Pull Request - State: closed - Opened by LotharukpongJS over 1 year ago - 1 comment

#39 - Minor changes to remove three warnings when running devtools::check()

Pull Request - State: closed - Opened by LotharukpongJS over 1 year ago - 1 comment

#38 - Updates to divergence_map and divergence_stratigraphy

Pull Request - State: closed - Opened by LotharukpongJS over 1 year ago

#38 - Updates to divergence_map and divergence_stratigraphy

Pull Request - State: closed - Opened by LotharukpongJS over 1 year ago

#37 - caught segfault, address cause 'invalid permissions'

Issue - State: open - Opened by awaisfarooq724 almost 2 years ago - 1 comment

#37 - caught segfault, address cause 'invalid permissions'

Issue - State: open - Opened by awaisfarooq724 almost 2 years ago - 1 comment

#36 - Integrate blastx and tblastx options

Issue - State: closed - Opened by qhelleu about 2 years ago - 2 comments

#36 - Integrate blastx and tblastx options

Issue - State: closed - Opened by qhelleu about 2 years ago - 2 comments

#35 - unable to install on R4.2

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

#35 - unable to install on R4.2

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

#34 - Missing sequences even with delete_corrupt_cds = FALSE

Issue - State: closed - Opened by ireneortega over 2 years ago - 8 comments

#34 - Missing sequences even with delete_corrupt_cds = FALSE

Issue - State: closed - Opened by ireneortega over 2 years ago - 8 comments

#33 - Missing headings blast_rec

Issue - State: open - Opened by ireneortega over 2 years ago - 7 comments

#33 - Missing headings blast_rec

Issue - State: open - Opened by ireneortega over 2 years ago - 7 comments

#32 - ERROR: number of input seqs differ (aa: 1; nuc: 2)!!

Issue - State: open - Opened by madzafv about 3 years ago - 1 comment

#32 - ERROR: number of input seqs differ (aa: 1; nuc: 2)!!

Issue - State: open - Opened by madzafv about 3 years ago - 1 comment

#31 - From orthologs to multiple align

Issue - State: closed - Opened by madzafv about 3 years ago - 8 comments
Labels: enhancement, help wanted

#31 - From orthologs to multiple align

Issue - State: closed - Opened by madzafv about 3 years ago - 8 comments
Labels: enhancement, help wanted

#30 - Clarification on pre-processing data and data types for dNdS estimation

Issue - State: closed - Opened by David-Peede about 3 years ago - 8 comments

#30 - Clarification on pre-processing data and data types for dNdS estimation

Issue - State: closed - Opened by David-Peede about 3 years ago - 8 comments

#29 - "path" option for Blast calls is non-functional

Issue - State: open - Opened by kushtun about 3 years ago - 1 comment

#29 - "path" option for Blast calls is non-functional

Issue - State: open - Opened by kushtun about 3 years ago - 1 comment

#28 - Ensembl gff does not work

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

#28 - Ensembl gff does not work

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

#27 - Installation error

Issue - State: closed - Opened by timregan over 3 years ago - 9 comments

#27 - Installation error

Issue - State: closed - Opened by timregan over 3 years ago - 9 comments

#24 - Control output value of orthologs function

Issue - State: open - Opened by janstrauss1 over 4 years ago - 1 comment
Labels: enhancement, question

#24 - Control output value of orthologs function

Issue - State: open - Opened by janstrauss1 over 4 years ago - 1 comment
Labels: enhancement, question

#23 - Extend filtering for lncRNA orthologs

Pull Request - State: closed - Opened by AlexGa over 4 years ago

#23 - Extend filtering for lncRNA orthologs

Pull Request - State: closed - Opened by AlexGa over 4 years ago

#22 - How to set PATH to OrthoFinder2 correctly?

Issue - State: open - Opened by janstrauss1 over 4 years ago - 5 comments

#22 - How to set PATH to OrthoFinder2 correctly?

Issue - State: open - Opened by janstrauss1 over 4 years ago - 5 comments

#21 - Problem running codon_aln with PAL2NAL

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

#21 - Problem running codon_aln with PAL2NAL

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

#20 - Update dplyr::group_map call

Pull Request - State: closed - Opened by AlexGa over 4 years ago

#20 - Update dplyr::group_map call

Pull Request - State: closed - Opened by AlexGa over 4 years ago

#19 - Minor changes/updates for generating ortholog tables

Pull Request - State: closed - Opened by AlexGa over 4 years ago

#19 - Minor changes/updates for generating ortholog tables

Pull Request - State: closed - Opened by AlexGa over 4 years ago

#18 - Running time

Issue - State: closed - Opened by CWYuan08 over 4 years ago - 2 comments

#18 - Running time

Issue - State: closed - Opened by CWYuan08 over 4 years ago - 2 comments

#17 - error back translating AA alignment to nucleotide pal2nal

Issue - State: closed - Opened by schultzm about 5 years ago - 1 comment

#16 - Can not download orthologr

Issue - State: closed - Opened by YUZHAN2019 about 5 years ago - 3 comments

#15 - How can I output blast_rec() results to file?

Issue - State: closed - Opened by paul-sheridan over 5 years ago - 2 comments

#14 - Problem calling `dNdS` on windows

Issue - State: closed - Opened by missuse over 5 years ago - 7 comments

#13 - Problem calling `blast` on windows

Issue - State: closed - Opened by missuse over 5 years ago - 9 comments

#12 - Problem calling `multi_aln` on windows

Issue - State: closed - Opened by missuse over 5 years ago - 3 comments

#11 - Error in ability to compile

Issue - State: closed - Opened by DanielleMStevens over 5 years ago - 1 comment

#10 - File input issue

Issue - State: closed - Opened by HirokiTomida about 6 years ago - 5 comments

#9 - Confirm that use of BLAST's `-max_target_seqs` is intentional

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

#8 - lots of CDS lost during orthology inference

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

#7 - Installation error

Issue - State: closed - Opened by SilviaHinojosa1983 over 6 years ago - 1 comment

#6 - clustalw in multi_aln

Issue - State: closed - Opened by aehr2 almost 7 years ago - 2 comments

#5 - Problem with input files in pal2nal

Issue - State: closed - Opened by harojm over 7 years ago - 2 comments

#4 - failed with dnds_est.method ="YN"

Issue - State: closed - Opened by microbiomeCat almost 8 years ago - 5 comments

#3 - Multiple cores

Issue - State: closed - Opened by vinaybaranwal almost 9 years ago - 5 comments

#2 - input files

Issue - State: closed - Opened by ghost about 9 years ago - 3 comments

#1 - Unable to install in Windows

Issue - State: closed - Opened by aromanowski over 9 years ago - 2 comments