EcoJulia/Microbiome.jl issues and pull requests

#144 - Improve efficiency of commjoin for large matrices

Issue - State: open - Opened by kescobo 5 months ago
Labels: enhancement

#143 - Selecting samples by vector of strings preserves order of original profile

Issue - State: open - Opened by kescobo 5 months ago
Labels: bug

#142 - Adopt views framework from SpatialEcology

Issue - State: closed - Opened by kescobo about 1 year ago - 3 comments
Labels: enhancement, Interop

#141 - Replace current metadata structure with DataAPI

Issue - State: open - Opened by kescobo about 1 year ago
Labels: enhancement

#140 - Remove deprecation and bump version

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

#139 - Get updates

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

#138 - Allow MultivariateStats v0.10

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

#137 - Faster methods for building metadata with subsets of fields

Issue - State: closed - Opened by kescobo almost 2 years ago
Labels: enhancement, Interop

#136 - Add Downstream tests for MicrobiomeAnalysis.jl

Issue - State: open - Opened by kescobo about 2 years ago
Labels: compat, ci

#135 - Improve speed of `shannon` and `ginisimpson`

Pull Request - State: closed - Opened by barucden about 2 years ago - 1 comment
Labels: enhancement

#134 - Add `by` option for `filter` to enable filtering on samples, matrix, etc.

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

#133 - Juliacon Tutorial

Pull Request - State: closed - Opened by kescobo over 2 years ago - 1 comment
Labels: docs

#132 - Juliacon tutorial outline

Pull Request - State: closed - Opened by anikaluo over 2 years ago - 3 comments

#131 - Code demo for JuliaCon presentation

Pull Request - State: closed - Opened by annelle-abatoni over 2 years ago - 1 comment

#130 - JuliaCon presentation

Issue - State: closed - Opened by kescobo over 2 years ago - 4 comments
Labels: docs

#129 - remove duplicate method

Pull Request - State: closed - Opened by kescobo over 2 years ago

#127 - mantel test

Issue - State: closed - Opened by EvoArt over 2 years ago - 2 comments
Labels: enhancement, Interop

#126 - Remove axis indices and nameddims

Pull Request - State: closed - Opened by kescobo over 2 years ago
Labels: compat, ci

#125 - Metabolites

Pull Request - State: closed - Opened by kescobo almost 3 years ago

#124 - add metabolite feature

Pull Request - State: closed - Opened by kescobo almost 3 years ago

#123 - Printing an empty comm profile throws error

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

#122 - Add Metabolite <: AbstractFeature

Issue - State: closed - Opened by kescobo almost 3 years ago
Labels: enhancement

#121 - Retest

Pull Request - State: closed - Opened by kescobo almost 3 years ago

#120 - add get method for whole community, and default for default

Pull Request - State: closed - Opened by kescobo almost 3 years ago

#119 - dont use rand in docs

Pull Request - State: closed - Opened by kescobo almost 3 years ago

#118 - update news

Pull Request - State: closed - Opened by kescobo almost 3 years ago
Labels: docs

#117 - Use Diversity.jl for alpha and beta diversity

Issue - State: open - Opened by kescobo almost 3 years ago
Labels: Interop

#116 - Update NEWS.md

Issue - State: closed - Opened by kescobo almost 3 years ago
Labels: docs

#115 - Joss review fixes

Pull Request - State: closed - Opened by kescobo almost 3 years ago - 1 comment
Labels: docs, I/O

#114 - documentation for `Microbiome.hasrank` and `Microbiome.Taxon`

Issue - State: closed - Opened by aguang almost 3 years ago
Labels: docs

#113 - support for biom format?

Issue - State: open - Opened by aguang almost 3 years ago - 3 comments
Labels: enhancement, I/O

#112 - vignette for data import

Issue - State: closed - Opened by aguang almost 3 years ago - 1 comment
Labels: docs

#111 - Can't run sample types docs s2 example

Issue - State: closed - Opened by aguang almost 3 years ago - 5 comments
Labels: bug, docs

#110 - Dependencies [minor issue]

Issue - State: closed - Opened by adRn-s almost 3 years ago - 4 comments
Labels: docs

#109 - Various fixes to tutorial

Pull Request - State: closed - Opened by kescobo almost 3 years ago

#108 - SparseArrays

Issue - State: closed - Opened by vanjakle almost 3 years ago - 1 comment

#107 - Dictionaries.jl in Microbiome.jl

Issue - State: closed - Opened by vanjakle almost 3 years ago - 1 comment

#106 - change group for BiobakeryUtils downstream tests

Pull Request - State: closed - Opened by kescobo almost 3 years ago

#105 - add missing dois

Pull Request - State: closed - Opened by kescobo almost 3 years ago

#104 - some readme typos

Pull Request - State: closed - Opened by kescobo almost 3 years ago

#103 - Add downstream package tests

Pull Request - State: closed - Opened by kescobo almost 3 years ago - 1 comment

#102 - EcoJulia transfer

Pull Request - State: closed - Opened by kescobo almost 3 years ago

#101 - Figures

Pull Request - State: closed - Opened by kescobo almost 3 years ago
Labels: docs

#100 - Manuscript

Pull Request - State: closed - Opened by annelle-abatoni almost 3 years ago - 4 comments
Labels: docs

#99 - manuscript edits/suggestions

Pull Request - State: closed - Opened by anikaluo almost 3 years ago - 1 comment

#98 - fix branch in gha-docs

Pull Request - State: closed - Opened by kescobo almost 3 years ago

#97 - Feature strings

Pull Request - State: closed - Opened by kescobo almost 3 years ago

#96 - use docs deploy action

Pull Request - State: closed - Opened by kescobo almost 3 years ago
Labels: bug, docs

#95 - Documenter broken - version incompatibility

Issue - State: closed - Opened by kescobo almost 3 years ago

#94 - Issue jubilee

Pull Request - State: closed - Opened by kescobo almost 3 years ago

#93 - grammar typo

Issue - State: closed - Opened by anikaluo almost 3 years ago

#92 - broken ref link

Issue - State: closed - Opened by anikaluo almost 3 years ago

#91 - `taxon` ref link

Issue - State: closed - Opened by anikaluo almost 3 years ago

#90 - master vs. main

Issue - State: closed - Opened by anikaluo almost 3 years ago - 1 comment
Labels: docs

#89 - Microbiome typos/edits

Pull Request - State: closed - Opened by anikaluo almost 3 years ago

#88 - Docs and tutorials

Pull Request - State: closed - Opened by kescobo almost 3 years ago - 2 comments

#87 - Indexing

Pull Request - State: closed - Opened by kescobo almost 3 years ago

#86 - add species string for gene families table output

Pull Request - State: closed - Opened by kescobo almost 3 years ago
Labels: enhancement

#85 - GeneFunction equality

Pull Request - State: closed - Opened by kescobo almost 3 years ago
Labels: enhancement

#83 - Manuscript

Pull Request - State: closed - Opened by kescobo about 3 years ago
Labels: docs

#82 - Adding docstrings to CP methods

Pull Request - State: closed - Opened by annelle-abatoni about 3 years ago - 2 comments
Labels: docs

#79 - Add generic filter for CommunityProfiles

Pull Request - State: closed - Opened by kescobo about 3 years ago
Labels: enhancement

#77 - Add cladefilter

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

#76 - Add docs for Dictionaries methods

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

#75 - Change add_metadata! for single samples to set! and insert!

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

#74 - Add dictionary methods to CommunityProfiles

Pull Request - State: closed - Opened by kescobo about 3 years ago - 2 comments
Labels: enhancement

#73 - change contributing link

Pull Request - State: closed - Opened by anikaluo about 3 years ago - 1 comment
Labels: docs

#72 - Method for bulk addition of metadata to a Community Profile

Pull Request - State: closed - Opened by kescobo about 3 years ago
Labels: enhancement

#71 - add constructor with dense matrix

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

#70 - add custom printing for abundance tables

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

#69 - Broken link to biojulia contribution guidelines

Issue - State: closed - Opened by EvoArt about 3 years ago - 2 comments
Labels: docs

#68 - Add function to partition gene function profile into stratified / unstratified

Issue - State: closed - Opened by kescobo about 3 years ago
Labels: enhancement

#67 - Add taxfilter/taxfilter! functions for community profiles

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

#66 - Metadata for CommunityProfiles

Pull Request - State: closed - Opened by kescobo about 3 years ago
Labels: enhancement

#65 - Add set! method for adding metadata to community profile

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

#64 - Bulk extraction of metadata

Issue - State: closed - Opened by kescobo about 3 years ago - 1 comment
Labels: enhancement

#63 - Bulk addition of metadata

Issue - State: closed - Opened by kescobo about 3 years ago
Labels: enhancement

#62 - Ensure round-tripping with DataFrames

Issue - State: closed - Opened by kescobo about 3 years ago - 2 comments
Labels: enhancement, compat

#61 - Add prevalence_filter

Pull Request - State: closed - Opened by kescobo about 3 years ago
Labels: enhancement

#60 - Re-implement @view from `ComMatrix` in SpatialEcology

Issue - State: open - Opened by kescobo about 3 years ago - 1 comment
Labels: enhancement

#59 - change ci to julia 1

Pull Request - State: closed - Opened by kescobo about 3 years ago
Labels: ci

#58 - Add function to join community profiles

Pull Request - State: closed - Opened by kescobo about 3 years ago - 1 comment
Labels: enhancement

#57 - Distance metrics

Pull Request - State: closed - Opened by pknight24 over 3 years ago - 5 comments

#56 - v0.7.0 release, version, news, etc

Pull Request - State: closed - Opened by kescobo almost 4 years ago
Labels: release

#55 - CompatHelper: bump compat for "Reexport" to "1.0"

Pull Request - State: closed - Opened by github-actions[bot] almost 4 years ago - 1 comment

#54 - Tables interface

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

#53 - CompatHelper: bump compat for "DataFrames" to "0.22"

Pull Request - State: closed - Opened by github-actions[bot] almost 4 years ago - 1 comment

#52 - TagBot trigger issue

Issue - State: closed - Opened by JuliaTagBot almost 4 years ago - 18 comments

#51 - update compat

Pull Request - State: closed - Opened by kescobo almost 4 years ago
Labels: compat

#50 - CompatHelper: bump compat for "MultivariateStats" to "0.8"

Pull Request - State: closed - Opened by github-actions[bot] almost 4 years ago

#49 - CompatHelper: bump compat for "DataFrames" to "0.22"

Pull Request - State: closed - Opened by github-actions[bot] almost 4 years ago

#48 - Updates

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

#47 - Fix Docs Build

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

#46 - CompatHelper: bump compat for "DataFrames" to "0.21"

Pull Request - State: closed - Opened by github-actions[bot] over 4 years ago

#45 - CompatHelper: bump compat for "StatsBase" to "0.33"

Pull Request - State: closed - Opened by github-actions[bot] over 4 years ago

#44 - Update SpatialEcology dependency

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

#43 - Bump version for compat

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

#42 - CompatHelper: bump compat for "SpatialEcology" to "0.9"

Pull Request - State: closed - Opened by github-actions[bot] over 4 years ago

#41 - CompatHelper: bump compat for "SpatialEcology" to "0.8"

Pull Request - State: closed - Opened by github-actions[bot] over 4 years ago

#40 - No Manifest file

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

GitHub / EcoJulia/Microbiome.jl issues and pull requests