dib-lab/kSpider issues and pull requests

#40 - Bump actions/download-artifact from 2 to 4.1.7 in /.github/workflows

Pull Request - State: closed - Opened by dependabot[bot] 5 months ago
Labels: dependencies

#39 - updated usage example

Issue - State: open - Opened by taylorreiter over 1 year ago - 16 comments

#38 - updated installation instructions

Issue - State: open - Opened by taylorreiter over 1 year ago - 3 comments

#37 - Community detections

Issue - State: open - Opened by mr-eyes almost 2 years ago

#36 - Bug fix, improvments and clustering validation

Pull Request - State: closed - Opened by mr-eyes almost 2 years ago

#35 - pairwise matrix validation in CI

Issue - State: open - Opened by mr-eyes almost 2 years ago

#34 - Test kmer sizes < 15

Issue - State: open - Opened by mr-eyes almost 2 years ago

#33 - Add sourmash as a plugin

Issue - State: open - Opened by mr-eyes about 2 years ago

#32 - Introduce strongly connected components in the clustering

Issue - State: open - Opened by mr-eyes about 2 years ago

#31 - More bugs fixed

Pull Request - State: closed - Opened by mr-eyes about 2 years ago

#30 - Build wheels for MACOS

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

#29 - Include kmer abundance to allow calculating Bray-Curtis dissimilarity

Issue - State: open - Opened by mr-eyes about 2 years ago
Labels: enhancement

#28 - Fixing bugs and adding features

Pull Request - State: closed - Opened by mr-eyes about 2 years ago - 1 comment

#27 - Indexing does not serialize correctly when using relative path

Issue - State: closed - Opened by mr-eyes about 2 years ago
Labels: bug

#26 - Sourmash into kSpider

Pull Request - State: closed - Opened by mr-eyes about 2 years ago

#25 - Get list of nodes with most undirected edges

Issue - State: open - Opened by mr-eyes about 2 years ago
Labels: enhancement

#24 - Explore other clustering methods

Issue - State: open - Opened by mr-eyes over 2 years ago

#23 - Link kSpider updates with sourmash docs

Issue - State: open - Opened by mr-eyes over 2 years ago

#22 - Indexing unified format (bins)

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

#21 - Add the brute-force mode directly into kSpider

Issue - State: open - Opened by mr-eyes over 2 years ago

#20 - Split parsing and indexing/pairwise

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

#19 - Optimizeing the clustering step

Pull Request - State: closed - Opened by mr-eyes over 2 years ago - 1 comment

#18 - Allow concurrent pairwise hashtable construction

Pull Request - State: closed - Opened by mr-eyes over 2 years ago - 1 comment

#17 - Supporting sourmash(#12)

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

#16 - Convert the clustering Python code to C++

Issue - State: open - Opened by mr-eyes over 2 years ago - 3 comments

#15 - Is containment threshold enough?

Issue - State: open - Opened by mr-eyes over 2 years ago

#14 - Allow concurrent construction of pairwise hashtable.

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

#13 - Consider serializing the pairwise hashtable

Issue - State: open - Opened by mr-eyes over 2 years ago

#12 - Supporting sourmash

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

#11 - Zoomable circle packing

Issue - State: open - Opened by mr-eyes over 2 years ago
Labels: enhancement

#10 - Adding sourmash support

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

#9 - kProcessor2 Integration

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

#8 - Add mode to assign new kmers to the nearest cluster

Issue - State: open - Opened by mr-eyes about 3 years ago

#7 - Update docs

Issue - State: open - Opened by mr-eyes about 3 years ago

#7 - Update docs

Issue - State: open - Opened by mr-eyes about 3 years ago

#6 - Core updates

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

#6 - Core updates

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

#5 - Add support for clustering Sourmash Signatures

Issue - State: closed - Opened by mr-eyes about 3 years ago - 1 comment

#4 - Implement export modes

Issue - State: closed - Opened by mr-eyes about 3 years ago

#4 - Implement export modes

Issue - State: closed - Opened by mr-eyes about 3 years ago

#3 - [WIP] New modes Improvements during PAG dev

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

#2 - CI Improvement

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

#2 - CI Improvement

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

#1 - [WIP] Support Protein/Dayhoff/Skipmers clustering

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

#1 - [WIP] Support Protein/Dayhoff/Skipmers clustering

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

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