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pathogen-embed
Create reduced dimension embeddings for pathogen sequences
https://pypi.org/project/pathogen-embed/
MIT License
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Allow pathogen-cluster to accept more than one distance matrix
#34
huddlej
opened
1 week ago
0
Enable clustering by distance matrix input
#33
huddlej
closed
2 weeks ago
0
Replace internal sorting with check for order
#32
huddlej
closed
1 month ago
0
Automatically pick SVD algorithm for PCA from data
#31
huddlej
closed
1 month ago
0
Release to PyPI with GitHub Actions
#30
huddlej
closed
1 month ago
0
Use inferred types for external embedding params
#29
huddlej
closed
1 month ago
0
Replace internal sort of alignments and distance matrices with a check for consistent record order across inputs
#28
huddlej
closed
1 month ago
0
Why is bioconda recipe more constrained than setup.py?
#27
corneliusroemer
opened
1 month ago
1
Relax scikit-learn constraint to support all of major version 1
#26
corneliusroemer
opened
1 month ago
1
Release to PyPI with GitHub Actions
#25
huddlej
closed
1 month ago
0
Build docs with sphinx instead of GitHub pages
#24
huddlej
opened
1 month ago
0
Add alternate encodings for PCA inputs
#23
huddlej
closed
1 month ago
0
Test alternate encodings of sequence data for PCA inputs
#22
huddlej
closed
1 month ago
0
Csv error check
#21
nandsra21
closed
3 months ago
0
pathogen-cluster: Export table of mutations per cluster
#20
huddlej
opened
4 months ago
0
Multiple alignment feature
#19
nandsra21
closed
2 months ago
1
Support Python 3.12
#18
huddlej
opened
4 months ago
0
adding changes to documentation to reflect changes to package
#17
nandsra21
closed
4 months ago
0
Add quickstart guide
#16
huddlej
closed
4 months ago
3
Alert user when input files are not formatted as CSVs
#15
huddlej
closed
3 months ago
0
Feature boxplot figure
#14
nandsra21
closed
4 months ago
1
Replace seaborn
#13
nandsra21
closed
4 months ago
0
Default learning rate fix
#12
nandsra21
closed
5 months ago
0
Display default parameters for subcommands of `pathogen-embed`
#11
huddlej
closed
5 months ago
0
embed: Support multiple input files for alignments and distance matrices
#10
huddlej
closed
2 months ago
1
Add a quickstart guide
#9
huddlej
closed
4 months ago
0
Add optional output from pathogen-embed that produces the boxplot figure of Euclidean by genetic distance
#8
huddlej
closed
4 months ago
0
Replace seaborn plotting with base matplotlib
#7
huddlej
closed
4 months ago
0
Add tests and fix bugs that surface
#6
huddlej
closed
6 months ago
0
t-sne init error
#5
jameshadfield
closed
6 months ago
1
Set default learning rate for t-SNE to "auto"
#4
huddlej
closed
5 months ago
1
Set random seed for PCA and MDS embeddings
#3
huddlej
closed
6 months ago
0
Create separate commands for embedding, clustering, and distance matrix creation
#2
nandsra21
closed
1 year ago
0
NumbaDeprecationWarning with latest dependencies, as "nopython" argument is not supplied to numba.jit
#1
nandsra21
closed
1 year ago
1