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Codon usage bias

bugSomething isn't workingSomething isn't working

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enhancementNew feature or requestNew feature or request

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Status: Open.

#160 In MatthewRalston/kmerdb;

· MatthewRalston opened on Jun 13, 2025

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Suitable for academic use

Currently using Deepseek R1 privately

dependenciesPull requests that update a dependency filePull requests that update a dependency file

documentationImprovements or additions to documentationImprovements or additions to documentation

good first issueGood for newcomersGood for newcomers

help wantedExtra attention is neededExtra attention is needed

invalidThis doesn't seem rightThis doesn't seem right

Status: Open.

#157 In MatthewRalston/kmerdb;

· MatthewRalston opened on Mar 20, 2025

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Suitable for academic use

Graph node labeling and traversal update

bugSomething isn't workingSomething isn't working

dependenciesPull requests that update a dependency filePull requests that update a dependency file

documentationImprovements or additions to documentationImprovements or additions to documentation

duplicateThis issue or pull request already existsThis issue or pull request already exists

invalidThis doesn't seem rightThis doesn't seem right

questionFurther information is requestedFurther information is requested

wontfixThis will not be worked onThis will not be worked on

Status: Open.

#153 In MatthewRalston/kmerdb;

· MatthewRalston opened on Aug 12, 2024

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v0.8 D2, node, edge, path formats, node/edge labeling, tetranucleotides

Kolmogorov complexity

bugSomething isn't workingSomething isn't working

documentationImprovements or additions to documentationImprovements or additions to documentation

invalidThis doesn't seem rightThis doesn't seem right

Status: Open.

#152 In MatthewRalston/kmerdb;

· MatthewRalston opened on Aug 12, 2024

·  

Suitable for academic use

Notes on mouse ibd

documentationImprovements or additions to documentationImprovements or additions to documentation

duplicateThis issue or pull request already existsThis issue or pull request already exists

invalidThis doesn't seem rightThis doesn't seem right

Status: Open.

#151 In MatthewRalston/kmerdb;

· MatthewRalston opened on Aug 12, 2024

·  

Suitable for academic use

Profile recomposition problem

bugSomething isn't workingSomething isn't working

enhancementNew feature or requestNew feature or request

help wantedExtra attention is neededExtra attention is needed

invalidThis doesn't seem rightThis doesn't seem right

wontfixThis will not be worked onThis will not be worked on

Status: Open.

#150 In MatthewRalston/kmerdb;

· MatthewRalston opened on Aug 12, 2024

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v0.7.2 stable, PyPI downloads

.kdbg format and variants

bugSomething isn't workingSomething isn't working

documentationImprovements or additions to documentationImprovements or additions to documentation

enhancementNew feature or requestNew feature or request

good first issueGood for newcomersGood for newcomers

help wantedExtra attention is neededExtra attention is needed

invalidThis doesn't seem rightThis doesn't seem right

questionFurther information is requestedFurther information is requested

wontfixThis will not be worked onThis will not be worked on

Status: Open.

#143 In MatthewRalston/kmerdb;

· MatthewRalston opened on Jul 14, 2024

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v0.8 D2, node, edge, path formats, node/edge labeling, tetranucleotides

Expectation functions

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documentationImprovements or additions to documentationImprovements or additions to documentation

enhancementNew feature or requestNew feature or request

questionFurther information is requestedFurther information is requested

Status: Open.

#142 In MatthewRalston/kmerdb;

· MatthewRalston opened on Jul 13, 2024

·  

v0.8 D2, node, edge, path formats, node/edge labeling, tetranucleotides

D2 metrics

bugSomething isn't workingSomething isn't working

dependenciesPull requests that update a dependency filePull requests that update a dependency file

documentationImprovements or additions to documentationImprovements or additions to documentation

duplicateThis issue or pull request already existsThis issue or pull request already exists

enhancementNew feature or requestNew feature or request

questionFurther information is requestedFurther information is requested

Status: Open.

#141 In MatthewRalston/kmerdb;

· MatthewRalston opened on Jul 13, 2024

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v0.8 D2, node, edge, path formats, node/edge labeling, tetranucleotides

Tetranucleotide bias and Karlin delta

bugSomething isn't workingSomething isn't working

documentationImprovements or additions to documentationImprovements or additions to documentation

enhancementNew feature or requestNew feature or request

questionFurther information is requestedFurther information is requested

wontfixThis will not be worked onThis will not be worked on

Status: Open.

#140 In MatthewRalston/kmerdb;

· MatthewRalston opened on Jul 13, 2024

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v0.8 D2, node, edge, path formats, node/edge labeling, tetranucleotides

Removing loose-ly deprecated parameters

bugSomething isn't workingSomething isn't working

documentationImprovements or additions to documentationImprovements or additions to documentation

enhancementNew feature or requestNew feature or request

good first issueGood for newcomersGood for newcomers

help wantedExtra attention is neededExtra attention is needed

invalidThis doesn't seem rightThis doesn't seem right

questionFurther information is requestedFurther information is requested

Status: Open.

#135 In MatthewRalston/kmerdb;

· MatthewRalston opened on Apr 4, 2024

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Interface Revision

Kmer.shred always returns sparse kmer_id/count array

documentationImprovements or additions to documentationImprovements or additions to documentation

Status: Open.

#134 In MatthewRalston/kmerdb;

· MatthewRalston opened on Apr 4, 2024

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V0.7 stable?