biocore/calour

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exploratory and interactive microbiome analyses based on heatmaps

Stars: 27
Forks: 20
Open beginner issues: 0
Indexed issues: 62

Dominant language: Python
License: BSD-3-Clause
Last GitHub push: Jan 27, 2025
Latest indexed: Sep 14, 2026
Contributing guide: Contributing guide
Code of conduct: No code of conduct
Beginner labels: No beginner labels indexed
PR merge metrics: No merged PRs in 30d

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62 open issues indexed

Please consider making the backend BIOM Open

biocore/calour#6 · 0 comments · 1 reaction · 0 assignees · Indexed Sep 14, 2026
filter == False Open

biocore/calour#14 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
matplotlib 2.0.0 dependency Open

wontfix

biocore/calour#15 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Port over niche_sort Open

biocore/calour#21 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Multiple comments on the current calour Open

biocore/calour#25 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
identify candidate contaminants Open

biocore/calour#27 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
default ignore your own experiment in enrichment analysis Open

biocore/calour#28 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
fix colors for jupyter gui dbbact annotations Open

biocore/calour#30 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
gnps clusterindex Open

biocore/calour#35 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
filter gnps to only keep annotated ones Open

biocore/calour#36 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Robust quantiles Open

enhancement

biocore/calour#38 · 5 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
add negate parameter to diff_abund and correlation functions Open

biocore/calour#41 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
support for continuous categories Open

enhancement

biocore/calour#57 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Change `sample_color_bars` to `sample_highlights`? Open

on deck question

biocore/calour#60 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
improve documentation for rescale Open

biocore/calour#64 · 1 comment · 0 reactions · 1 assignee · Indexed Sep 14, 2026
test image for readme Open

biocore/calour#80 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
allow io.read() to read bioms and metadata files in memory Open

biocore/calour#89 · 7 comments · 1 reaction · 0 assignees · Indexed Sep 14, 2026
passing extra features to feature_metadata silently produces incorrect metadata Open

biocore/calour#95 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Running in Jupyter Lab breaks visualization Open

biocore/calour#122 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
"find_lowest_taxonomy" producing "s__" Open

biocore/calour#129 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Can calour detect multipile groups differential abundance? Open

biocore/calour#136 · 5 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
download button appears to be broken Open

biocore/calour#157 · 4 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Paired heatmaps Open

biocore/calour#164 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
add tracker bar for x and y in heatmap to show location when zoomed Open

enhancement

biocore/calour#166 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
color scale Open

biocore/calour#172 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
minor issues Open

biocore/calour#200 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
error when supplying 'sep' to sample_metadata_kwargs in readms() Open

bug

biocore/calour#202 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 14, 2026
create ratioexperiment class Open

enhancement

biocore/calour#205 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 14, 2026
add un-normalize to save() Open

enhancement

biocore/calour#206 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 14, 2026
get rid of skbio Open

enhancement

biocore/calour#212 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 14, 2026
add per row normalization to heatmap Open

enhancement

biocore/calour#223 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
problem with plot normalization for non ampliconexperiment Open

biocore/calour#229 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
filter_mean_abundance on unnormalized data Open

bug

biocore/calour#232 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Add an option to read metadata from csv files Open

biocore/calour#234 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
normalize diff_abundance results with rank to -1/1 Open

biocore/calour#242 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
first and last feature in heatmap Open

biocore/calour#243 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
export_heatmap enable different field for taxonomy and heatmap y-axis Open

enhancement

biocore/calour#251 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
io.read() has the sep='\t' set so cannot re-set it in the sample_metadata_kwargs Open

bug

biocore/calour#258 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
norm() for heatmap - maybe supply also a string option for "linear" or "log" Open

enhancement

biocore/calour#259 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
enable single value input in filter_by_metadata() Open

biocore/calour#261 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
filter_prevalence() field parameter not working Open

bug

biocore/calour#262 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
raise warning if value does not exist in diff_abundance Open

biocore/calour#264 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Problem with rarifying unnormalized experiments Open

bug

biocore/calour#265 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Installation problems Open

biocore/calour#267 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
raise appropriate error when plotting an empty experiment Open

biocore/calour#268 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
enable rotation for barx_label_kwargs in plot() Open

biocore/calour#269 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
set default (white) for missing colors in barx_colors in plot() Open

biocore/calour#270 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
missing documentation in the calour .io docs for to/from pandas Open

enhancement

biocore/calour#282 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
filter_samples does not work when supplying values as a numpy array Open

bug

biocore/calour#283 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
when doing cluster_features for metaphlan output (shotgun metagenomics), need to set different presence threshold Open

biocore/calour#284 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026

biocore/calour

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