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SBRG
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pymodulon
Python package for analyzing and visualizing iModulons
MIT License
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#71
sapoudel
closed
3 years ago
0
make_prots_db now handles multiple fasta files. Tests updated to cove…
#70
sapoudel
closed
3 years ago
0
Test functions for enrichments.py
#69
talbulus
closed
3 years ago
0
Allow users to enter multiple fasta files to make_prots_db
#68
sapoudel
closed
3 years ago
0
Make_prots_db doesn't work with NCBI files
#67
sapoudel
closed
3 years ago
1
Create .readthedocs.yaml
#66
avsastry
closed
3 years ago
0
Changed doc strings for enrichment, util, imoddb, example, enrich, and plotting
#65
Reosu
closed
3 years ago
0
Changed Docstrings of compare, core, and io
#64
Reosu
closed
3 years ago
1
Update make_prots and BBH functions to play nice with NCBI
#63
avsastry
closed
3 years ago
1
Add fit_metric=None in plotting.scatterplot
#62
avsastry
closed
3 years ago
0
Make a __repr__ function for the IcaData object
#61
avsastry
opened
3 years ago
1
Update docstrings and remove typing
#60
avsastry
closed
3 years ago
1
explained_variance improvements
#59
avsastry
closed
3 years ago
2
Italicize gene names in plot_gene_weights
#58
avsastry
closed
3 years ago
0
Dima fix
#57
Reosu
closed
3 years ago
0
Fixed bug in plot_dima associated with labeling
#56
Reosu
closed
3 years ago
0
Add evidence levels for regulon enrichments
#55
avsastry
closed
3 years ago
1
num2name() is now case insensitive, cog_color bug fix w/out setters, increased iterations for curve_fit
#54
kevin-rychel
closed
3 years ago
0
Update imodulondb to match master
#53
kevin-rychel
closed
3 years ago
0
Fixed a COG color error if the gene table is unexpectedly updated
#52
kevin-rychel
closed
3 years ago
0
Implement automated activity classification from experimental metadata
#51
avsastry
closed
3 years ago
1
Move plasmid gene locations to end of iModulon gene scatter
#50
avsastry
opened
3 years ago
0
Fixed minor errors in iModulonDB_setup.py
#49
kevin-rychel
closed
3 years ago
0
Minor bug fixes
#48
kevin-rychel
closed
3 years ago
0
Change certain warnings to log.warning
#47
avsastry
closed
3 years ago
2
Add option in get_prots function to use 'old_locus_tags'
#46
sapoudel
closed
3 years ago
0
Added iModulonDB Compatibility
#45
kevin-rychel
closed
3 years ago
0
Incorrect/bad dimensionality recommendation
#44
sapoudel
closed
3 years ago
1
Highlighting Differential Genes in the DIMA plots
#43
Reosu
closed
3 years ago
0
Setter for iModulon names
#42
sapoudel
closed
3 years ago
1
Add pre-commit
#41
avsastry
closed
3 years ago
0
For barplot base figure, automatically highlight project if it's the only project selected
#40
avsastry
closed
3 years ago
1
Add error message if threshold method is not 'kmeans' or 'dagostino'
#39
avsastry
closed
3 years ago
1
Add ica_data objects for published datasets
#38
avsastry
closed
3 years ago
7
Use iModulons to interpret new data
#37
avsastry
closed
3 years ago
1
Update IO to use gzip
#36
camlam
closed
4 years ago
0
ZIP handling for IO functions
#35
camlam
closed
4 years ago
1
Clustering/DIMCA
#34
camlam
closed
4 years ago
0
Add MEME integration
#33
avsastry
closed
3 years ago
0
Recovered variance
#32
avsastry
closed
4 years ago
1
Timeseries visualizations
#31
avsastry
closed
2 years ago
0
Previous code identifies different optimal thresholds
#30
avsastry
closed
3 years ago
2
plot_gene_weights() Not working
#29
kevin-rychel
closed
4 years ago
2
Org compare
#28
Reosu
closed
4 years ago
0
Org compare
#27
Reosu
closed
4 years ago
0
IO Error in pymodulon
#26
avsastry
closed
4 years ago
2
compute_trn_enrichment() does not allow for unnamed iModulons
#25
siddC
closed
3 years ago
4
Keep parity with master
#24
siddC
closed
4 years ago
0
Gene weight x axis
#23
siddC
closed
4 years ago
0
Cross-species Gene Weight Comparison
#22
siddC
closed
4 years ago
1
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