Ecosyste.ms: Issues

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GitHub / CSBiology/BioFSharp issues and pull requests

#136 - Add RNA Seq normalization methods

Pull Request - State: closed - Opened by ScheidTo 10 months ago - 3 comments

#135 - [Docs] Was image created by mermaid?

Issue - State: closed - Opened by Fxplorer 11 months ago - 1 comment
Labels: documentation

#134 - [Feature Request] Addition of adjusted PValues to GSEA Result

Issue - State: open - Opened by bvenn about 2 years ago
Labels: FeatureRequest

#133 - Update GSEA docu

Pull Request - State: open - Opened by bvenn about 2 years ago

#132 - [BUG] Hypergeometric Distribution CDF update will change input

Issue - State: open - Opened by Freymaurer over 2 years ago
Labels: bug

#131 - [Feature Request] OBO parser improvements

Issue - State: open - Opened by HLWeil over 2 years ago
Labels: FeatureRequest

#130 - [BUG] Pairwise alignment does not correctly handle gap opening costs

Issue - State: open - Opened by HLWeil almost 3 years ago
Labels: bug

#129 - add obo verbosity

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

#128 - OBO parser verbosity

Issue - State: closed - Opened by bvenn about 3 years ago

#127 - Bump SharpZipLib from 1.3.1 to 1.3.3 in /src/BioFSharp.BioContainers

Pull Request - State: open - Opened by dependabot[bot] about 3 years ago
Labels: dependencies

#126 - update references

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

#125 - #124 fix gsea typo

Pull Request - State: closed - Opened by bvenn about 3 years ago - 1 comment

#124 - Ontology enrichment field name need revision

Issue - State: closed - Opened by bvenn about 3 years ago

#123 - [WIP] Update docs

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

#122 - [BUG] Using pretty printers on BioSeq after translation results in an empty source sequence

Issue - State: open - Opened by kMutagene over 3 years ago - 5 comments
Labels: bug

#121 - add mid pvalue description to GSEA documentation

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

#120 - [Feature Request] Add more Proteases

Issue - State: open - Opened by ZimmerD over 3 years ago
Labels: priority-low, FeatureRequest

#119 - [Feature Request] Update or move dppop

Issue - State: open - Opened by kMutagene over 3 years ago
Labels: priority-low, FeatureRequest, project-ML

#118 - [BUG] Obo.parseOboTerms too strict about parsing whitespace

Issue - State: open - Opened by Freymaurer almost 4 years ago
Labels: bug

#117 - [Feature Request] Seamless phylogenetic tree building from sequences using ClustalO wrapper

Issue - State: open - Opened by HLWeil almost 4 years ago
Labels: project-IO, FeatureRequest

#116 - [BUG] ClustalO wrapper example from the docs is not working correctly

Issue - State: open - Opened by kMutagene almost 4 years ago - 8 comments
Labels: bug, project-IO

#115 - Fix typo: monoicsotopic -> monoisotopic

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

#114 - Fix typo: monoicsotopic -> monoisotopic

Pull Request - State: closed - Opened by dawedawe almost 4 years ago - 2 comments

#113 - [BUG] Fasta writer EOL may cause downstream tools being unable to parse the fasta

Issue - State: open - Opened by kMutagene almost 4 years ago
Labels: bug, project-IO, priority-low

#112 - BioFSharp Project rejuvenation

Issue - State: open - Opened by kMutagene almost 4 years ago - 3 comments
Labels: priority-high, project-all

#111 - [BUG] BioFSharp.IO.Obo.parseOboTerms parsing error with ':'

Issue - State: closed - Opened by Freymaurer about 4 years ago
Labels: bug

#110 - #30: Add phyl tree tests

Pull Request - State: closed - Opened by graemevissers over 4 years ago - 1 comment

#109 - #30: Add nucleotide tests

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

#108 - #30: Add amino acid tests

Pull Request - State: closed - Opened by graemevissers over 4 years ago - 2 comments

#107 - #30: Add AminoAcids tests

Pull Request - State: closed - Opened by graemevissers over 4 years ago - 1 comment

#106 - #30 : Add BioSeq tests

Pull Request - State: closed - Opened by graemevissers over 4 years ago - 1 comment

#105 - [Feature Request] Add installation procedure to Readme

Issue - State: open - Opened by ZimmerD over 4 years ago
Labels: FeatureRequest

#104 - [Feature Request] Rework ModificationInfo's implementation of IBioItem

Issue - State: open - Opened by kMutagene over 4 years ago
Labels: up-for-grabs, FeatureRequest

#103 - #30 : Add bio list tests

Pull Request - State: closed - Opened by graemevissers over 4 years ago - 1 comment

#102 - [BUG] Include all possible bin sizes within GSEA (0 and 1)

Issue - State: open - Opened by bvenn over 4 years ago
Labels: bug

#101 - Add bio array tests

Pull Request - State: closed - Opened by graemevissers over 4 years ago - 1 comment

#100 - Add bio array tests

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

#99 - Move tests to netcore and add code coverage via altcover

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

#98 - Digestion

Pull Request - State: closed - Opened by ZimmerD over 4 years ago - 1 comment

#97 - [Feature Request] Complete Digestion module

Issue - State: closed - Opened by ZimmerD over 4 years ago - 1 comment
Labels: FeatureRequest

#96 - [Docs] Reference to FastA Histrogram is incorrect

Issue - State: open - Opened by bvenn over 4 years ago - 1 comment
Labels: documentation

#95 - [Feature Request]Rework BioCollections

Issue - State: open - Opened by kMutagene over 4 years ago
Labels: project-Core, FeatureRequest

#94 - [Feature Request]Extend OBO parser to fully support the obo flat file 1.4 specifications

Issue - State: open - Opened by kMutagene almost 5 years ago
Labels: project-IO, priority-low, FeatureRequest

#93 - [BUG]OBO parser skips all relationships but the last

Issue - State: closed - Opened by kMutagene almost 5 years ago - 3 comments
Labels: bug, project-IO, priority-high

#92 - [Feature Request]Add Entrez query builder

Issue - State: open - Opened by kMutagene almost 5 years ago
Labels: project-BioDB, priority-low, FeatureRequest

#91 - Sync with developer - dont squash developer commits again :(

Pull Request - State: closed - Opened by kMutagene almost 5 years ago

#90 - [Feature Request] Move tests to .net core

Issue - State: closed - Opened by kMutagene almost 5 years ago - 1 comment
Labels: FeatureRequest

#89 - completely revamp buildchains

Pull Request - State: closed - Opened by kMutagene almost 5 years ago

#88 - Update with changes from developer for 1.2.0

Pull Request - State: closed - Opened by kMutagene almost 5 years ago

#87 - [Feature Request] Add high-level functionality for Entrez cgi DSLs

Issue - State: open - Opened by kMutagene almost 5 years ago
Labels: up-for-grabs, project-BioDB, FeatureRequest

#86 - Update with changes from developer for 1.1.0

Pull Request - State: closed - Opened by kMutagene almost 5 years ago

#85 - [BUG] BioContainer STDOut is not attached to FSI, only gets returned when container tasks are finished/aborted

Issue - State: open - Opened by kMutagene almost 5 years ago
Labels: bug, project-BioContainers

#84 - [Feature Request]Implement Entrez query construction and databases queries

Issue - State: closed - Opened by kMutagene almost 5 years ago
Labels: up-for-grabs, project-BioDB, FeatureRequest

#83 - Sync master with developer for 1.0.03

Pull Request - State: closed - Opened by kMutagene almost 5 years ago

#82 - improve Sailent.compute characterization speed

Pull Request - State: closed - Opened by HLWeil almost 5 years ago - 1 comment

#81 - Improve docs

Pull Request - State: closed - Opened by kMutagene almost 5 years ago

#80 - Travis fix

Pull Request - State: closed - Opened by kMutagene almost 5 years ago

#79 - Update master with changes from Developer for 1.0.02

Pull Request - State: closed - Opened by kMutagene almost 5 years ago

#78 - Migrate to new dotnet build chain

Pull Request - State: closed - Opened by kMutagene about 5 years ago

#77 - [Feature Request] Move to new and simplified dotnet build process

Issue - State: closed - Opened by kMutagene about 5 years ago
Labels: priority-high, FeatureRequest

#76 - Update master with changes up to 1.0.0 from developer

Pull Request - State: closed - Opened by kMutagene over 5 years ago

#75 - [Feature Request] Optimize Sailent to increase computation speed

Issue - State: closed - Opened by kMutagene over 5 years ago - 3 comments
Labels: project-Stats, FeatureRequest

#74 - [Feature Request] Increase verbosity of Sailent.compute

Issue - State: closed - Opened by ZimmerD over 5 years ago - 5 comments
Labels: project-Stats, FeatureRequest

#73 - [Feature Request] Automatically take care if Image exists with correct tag for biocontainers

Issue - State: open - Opened by kMutagene over 5 years ago
Labels: FeatureRequest, project-BioContainers

#72 - [BUG]SOFT Parser skips entities

Issue - State: closed - Opened by kMutagene over 5 years ago - 1 comment
Labels: bug, project-IO

#71 - [BUG] Wrong versions in nuget packages built with Paket.pack

Issue - State: closed - Opened by kMutagene over 5 years ago - 1 comment
Labels: bug, priority-high, project-all

#70 - [Feature Request]Replace deprecated FAKE calls in the build script

Issue - State: closed - Opened by kMutagene over 5 years ago - 1 comment
Labels: project-all, FeatureRequest

#69 - Fix paket.exe not found when starting the nuget fake target

Pull Request - State: closed - Opened by kMutagene over 5 years ago - 1 comment

#68 - [BUG] Paket.exe missing when building on a clean(with all necessary frameworks and tools) machine

Issue - State: closed - Opened by kMutagene over 5 years ago - 1 comment
Labels: bug, project-all, Needs Refactoring

#67 - [Docs] Some formatted outputs are missing

Issue - State: open - Opened by kMutagene over 5 years ago - 2 comments
Labels: documentation, priority-medium

#66 - [BUG] Nucleotides.antiparallel delivers unexpected results

Issue - State: closed - Opened by rolfsuter over 5 years ago - 3 comments
Labels: bug

#65 - [Docs] Clarify Nucleotides.inverse function

Issue - State: closed - Opened by rolfsuter over 5 years ago - 3 comments
Labels: project-Core, Needs Refactoring

#64 - Add moFF to BioTools

Pull Request - State: closed - Opened by Joott over 5 years ago

#63 - Add moFF to BioTools

Pull Request - State: closed - Opened by Joott over 5 years ago

#62 - [Feature Request] Improve Formula parsing/printing consistency

Issue - State: open - Opened by kMutagene over 5 years ago
Labels: project-Core, priority-medium, FeatureRequest

#61 - [Feature Request] Rework alignment

Issue - State: open - Opened by HLWeil over 5 years ago - 2 comments
Labels: priority-medium, FeatureRequest

#60 - PSI-BLAST command

Pull Request - State: closed - Opened by MikhayN over 5 years ago - 1 comment

#59 - Update paket.lock

Pull Request - State: closed - Opened by Joott over 5 years ago

#58 - [Feature Request] Documentation for Ontology Enrichment

Issue - State: closed - Opened by Freymaurer over 5 years ago - 1 comment
Labels: FeatureRequest

#57 - [Docs] Add ImgP docs

Issue - State: open - Opened by kMutagene over 5 years ago
Labels: documentation, project-ImgP

#56 - [Docs] Add BioFSharp.ML docs

Issue - State: open - Opened by kMutagene over 5 years ago
Labels: documentation, project-ML

#55 - Add most important BioTools docker APIs for 1.0.0

Issue - State: open - Opened by kMutagene over 5 years ago - 1 comment
Labels: priority-high, FeatureRequest, project-BioContainers

#54 - [Docs] Add BioTools docs

Issue - State: closed - Opened by kMutagene over 5 years ago
Labels: documentation, project-BioContainers

#53 - Update master with changes until 0.1.0 from developer

Pull Request - State: closed - Opened by kMutagene over 5 years ago

#52 - [BUG] FastA-Writer appends to file instead of recreating it

Issue - State: closed - Opened by bvenn over 5 years ago - 1 comment
Labels: bug, project-IO

#51 - PWM

Pull Request - State: closed - Opened by Etschbeijer almost 6 years ago - 4 comments

#50 - Addition of tools for statistical analysis of biological sequences

Issue - State: open - Opened by Etschbeijer almost 6 years ago
Labels: FeatureRequest

#49 - Should 'release' build target require confirmation?

Issue - State: closed - Opened by bvenn almost 6 years ago - 1 comment
Labels: question, priority-medium

#48 - FastA to GFF3 conversion

Issue - State: closed - Opened by HLWeil almost 6 years ago - 3 comments
Labels: project-Core, project-IO, priority-medium, FeatureRequest

#47 - [BUG] GFF3-Writer appends to file instead of recreating it

Issue - State: closed - Opened by bvenn almost 6 years ago
Labels: bug, project-IO

#46 - fix build target "Nuget"

Pull Request - State: closed - Opened by ZimmerD almost 6 years ago
Labels: project-structure, priority-high

#45 - [Feature Request] Missing GAF Parser

Issue - State: closed - Opened by bvenn almost 6 years ago - 1 comment
Labels: project-IO, priority-low, FeatureRequest

#44 - Documentation Typo fixing

Pull Request - State: closed - Opened by dcoull almost 6 years ago - 1 comment

#40 - Addition of various biotool docker container APIs to the BioTools project

Issue - State: open - Opened by kMutagene about 6 years ago - 1 comment
Labels: up-for-grabs, priority-medium, project-BioContainers

#36 - [BUG] Fasta reader cant read from gzip file

Issue - State: closed - Opened by kMutagene about 6 years ago - 1 comment
Labels: bug, up-for-grabs, project-IO, priority-medium

#35 - [BUG] OboParser neglects first occurences of alt_ids

Issue - State: closed - Opened by bvenn about 6 years ago
Labels: bug, up-for-grabs, project-IO, priority-medium

#34 - Add pretty printers for common biological file formats

Issue - State: open - Opened by kMutagene about 6 years ago - 1 comment
Labels: up-for-grabs, project-all, good first issue

#32 - Documentation cleanup and extension

Issue - State: open - Opened by kMutagene over 6 years ago
Labels: priority-medium, project-all

#30 - Addition of Unit Testing for all projects

Issue - State: open - Opened by kMutagene over 6 years ago - 1 comment
Labels: up-for-grabs, priority-medium, project-all, good first issue

#29 - Refactoring and inclusion of our next generation sequencing pipeline

Issue - State: closed - Opened by kMutagene over 6 years ago - 2 comments
Labels: project-IO, priority-medium