Ecosyste.ms: Issues

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GitHub / gamcil/clinker issues and pull requests

#115 - Can we adjust the identity scale in clinker?

Issue - State: open - Opened by fsnibs10 3 months ago - 1 comment

#114 - ✨ feat: enhancement #113

Pull Request - State: closed - Opened by Aurorabili 3 months ago - 1 comment

#113 - Support for including multiple sequences in genbank files

Issue - State: closed - Opened by Aurorabili 3 months ago - 2 comments

#112 - Can different domains within a gene also be applicable?

Issue - State: open - Opened by xubiy 5 months ago - 2 comments

#111 - Running clinker via spyder

Issue - State: open - Opened by Wanjofu 6 months ago

#110 - Renaming coding sequence back to gene number

Issue - State: open - Opened by timeresistance1996 6 months ago - 3 comments

#109 - Broken pipe error when using clinker to plot gene clusters

Issue - State: closed - Opened by jonng2024 7 months ago - 2 comments

#108 - Gene and species limit

Issue - State: closed - Opened by IzenR 8 months ago - 1 comment

#107 - try example encouter error

Issue - State: open - Opened by nongbaoting 11 months ago

#106 - Problem with -gf and -cm parameteres

Issue - State: open - Opened by mattbird567 about 1 year ago - 3 comments

#105 - -gf/--gene_functions not working?

Issue - State: closed - Opened by mattbird567 about 1 year ago

#103 - Locus inversion showing incorrect locations

Issue - State: open - Opened by AthinaGav about 1 year ago

#102 - some issues for -mo --matrix_out parameter

Issue - State: open - Opened by Yuki0902 about 1 year ago - 2 comments

#101 - The output result has no information

Issue - State: closed - Opened by yuezhiTang about 1 year ago - 4 comments

#100 - Errors in using gff and faa file

Issue - State: open - Opened by Xinpeng021001 over 1 year ago - 1 comment

#99 - Error in clinker HTML plotting function

Issue - State: open - Opened by Nitin123-4 over 1 year ago

#98 - ValueError: not enough values to unpack (expected 2, got 1)

Issue - State: open - Opened by neelam19051 almost 2 years ago

#96 - How to visualize a gene on a large chromosome?

Issue - State: closed - Opened by JulieDaz almost 2 years ago

#95 - the legend

Issue - State: closed - Opened by Oelsakha almost 2 years ago - 4 comments

#94 - update 0.0.28

Issue - State: open - Opened by oclaisse almost 2 years ago - 3 comments

#93 - Can't save changes to session

Issue - State: closed - Opened by camilo-monge almost 2 years ago - 2 comments

#92 - Similarity score and plotting

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

#91 - Conda package errors

Issue - State: closed - Opened by Anto007 about 2 years ago - 3 comments

#90 - protein groups and similarity

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

#89 - Clinker issue: Blocks instead of arrows

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

#88 - How to only generate html files?

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

#87 - clustermap loading slow

Issue - State: closed - Opened by yzjie6 over 2 years ago - 1 comment

#86 - docs on gff+fasta

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

#85 - Export SVG instead of html

Issue - State: open - Opened by innovate-invent over 2 years ago

#84 - Clinker usage

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

#83 - Clink does not show any features

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

#82 - Feature request: set font style, link color and gene color

Issue - State: open - Opened by koolape over 2 years ago

#81 - Using clinker in windows Cmd shell, only alignement of last name sequences

Issue - State: open - Opened by CWoudstra over 2 years ago - 6 comments

#80 - Questions

Issue - State: open - Opened by yga18 over 2 years ago

#79 - Circular sequence panning

Issue - State: closed - Opened by erinyoung over 2 years ago

#78 - How to load a session file ?

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

#77 - Truncating the middle of gene clusters & gene group legend

Issue - State: open - Opened by wearegroot91 almost 3 years ago - 2 comments

#76 - Grouping by function rather than similarity

Pull Request - State: closed - Opened by gamcil about 3 years ago

#75 - ERROR in matrix.select

Issue - State: closed - Opened by dooguypapua about 3 years ago - 2 comments

#73 - Gene label type issue

Issue - State: open - Opened by RvV1979 over 3 years ago

#72 - Clinker just stalls without producing output?

Issue - State: open - Opened by Arzamasov over 3 years ago - 7 comments

#71 - gene model colouring issue

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

#70 - Align Error: seq contains letters not in the alphabet

Issue - State: closed - Opened by LeoBusse over 3 years ago - 2 comments

#69 - cluster similarity matrix

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

#68 - Error in align

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

#67 - GFF+Fasta files without line wrapping doesn't display properly

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

#66 - Gene labels not extracting correctly

Issue - State: open - Opened by sean-bam over 3 years ago

#65 - Elaborate on the input file contents

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

#64 - Error in plot Visualization

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

#62 - [Feature request] option to indicate subsection of Genbank file

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

#60 - Running Clinker on a Server?

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

#59 - Error when using gff file as input

Issue - State: open - Opened by TsumaR over 3 years ago

#58 - Add scaffold ranges

Pull Request - State: closed - Opened by gamcil over 3 years ago

#57 - Feature Request: Incomplete/disrupted genes in the figure

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

#56 - Add scaffold ranges

Pull Request - State: closed - Opened by gamcil over 3 years ago

#55 - extend sub matrix alphabets to avoid exceptions during alignment

Pull Request - State: closed - Opened by gamcil over 3 years ago

#54 - fix mock div element when saving svg

Pull Request - State: closed - Opened by gamcil over 3 years ago

#53 - Colour additions

Pull Request - State: closed - Opened by gamcil over 3 years ago

#52 - Group restoration when inst. Globaligner from dict

Pull Request - State: closed - Opened by lukas-val over 3 years ago - 1 comment

#51 - Groups are not restored during session loading

Issue - State: closed - Opened by lukas-val over 3 years ago - 2 comments

#50 - Replace consolidation with a disjoint-set data structure

Pull Request - State: closed - Opened by althonos over 3 years ago - 1 comment

#49 - RecursionError in `clinker.align.consolidate` (and a proposed fix)

Issue - State: closed - Opened by althonos over 3 years ago - 2 comments

#48 - Maximum recursion depth exceeded

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

#47 - Groups refactor

Pull Request - State: closed - Opened by gamcil almost 4 years ago

#46 - Changing color of a gene to a specific desired color

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

#45 - "This SVG is not valid, validate it before opening"

Issue - State: closed - Opened by kforcone almost 4 years ago - 2 comments

#44 - Fix gff empty gene

Pull Request - State: closed - Opened by gamcil almost 4 years ago

#43 - add default values to arguments, example usage to help

Pull Request - State: closed - Opened by gamcil almost 4 years ago

#42 - Fix `format_links` writing query instead of target name in target column

Pull Request - State: closed - Opened by althonos almost 4 years ago - 1 comment

#41 - Examples in help

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

#40 - update citation

Pull Request - State: closed - Opened by gamcil almost 4 years ago

#39 - Example GFF files

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

#38 - Feature request: cluster granularity settings

Issue - State: open - Opened by RvV1979 almost 4 years ago
Labels: enhancement

#37 - Feature request: categorial color scheme for cluster groups

Issue - State: open - Opened by RvV1979 almost 4 years ago
Labels: enhancement

#36 - Feature request: setting sequence window

Issue - State: closed - Opened by RvV1979 almost 4 years ago - 3 comments
Labels: enhancement

#35 - Issue with multi-exon genes

Issue - State: open - Opened by RvV1979 almost 4 years ago

#33 - Addition to help text: Double click flips contig

Issue - State: closed - Opened by passdan almost 4 years ago - 2 comments

#31 - Add info for conda install

Pull Request - State: closed - Opened by rpetit3 almost 4 years ago - 1 comment

#30 - How to adjust the distance between the sample name and the sequence in clinker?

Issue - State: closed - Opened by jeep3 almost 4 years ago - 2 comments

#29 - Bioconda submission naming

Issue - State: closed - Opened by rpetit3 almost 4 years ago - 2 comments

#28 - Issue with anaconda3 on mac and Clinker

Issue - State: closed - Opened by lgannon248 almost 4 years ago - 3 comments

#27 - How can I get GTF files into this type of software

Issue - State: closed - Opened by bioinfowheat almost 4 years ago - 8 comments

#26 - Possible errors when running clinker v0.0.11 with GenBank files from MiBIG

Issue - State: closed - Opened by 0x1d4e almost 4 years ago - 4 comments

#25 - Feature request: match gene order

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

#24 - Add GFF3+FASTA parser

Pull Request - State: closed - Opened by gamcil almost 4 years ago

#23 - Link lines, unscaled genes

Pull Request - State: closed - Opened by gamcil almost 4 years ago

#22 - Implement parallel computing of alignments

Pull Request - State: closed - Opened by althonos almost 4 years ago - 4 comments

#21 - prohibitively slow performance

Issue - State: open - Opened by marade almost 4 years ago - 9 comments

#20 - pip install clinker - ERROR: Command errored out with exit status 1

Issue - State: closed - Opened by mafeeney almost 4 years ago - 2 comments

#19 - pip3 install clinker instead pip install - Ubuntu 20.04 LTS

Issue - State: closed - Opened by JuanMartinezV almost 4 years ago - 1 comment

#18 - Refactor globaligner

Pull Request - State: closed - Opened by gamcil almost 4 years ago

#17 - Possible to ignore coordinates and show gene order only?

Issue - State: closed - Opened by RvV1979 almost 4 years ago - 7 comments

#16 - fix divide-by-zero when creating matrix with empty alignments

Pull Request - State: closed - Opened by gamcil almost 4 years ago