2024-12-03

What's Changed

• Create shell script for wilms-06 workflow by @sjspielman in #817
• Update the feature/wilms-tumor-azimuth-06 branch by @sjspielman in #823
• Wilms 06 update: script to prepare fetal references by @sjspielman in #814
• Update cell-type-wilms-tumor-06 workflow by @sjspielman in #827
• Merge main into feature/wilms-tumor-06-azimuth by @sjspielman in #834
• Merge main into wilms azimuth branch by @sjspielman in #851
• Adapt Azimuth code for Wilms label transfer by @sjspielman in #843
• 1/n: Update wilms 06 module by @sjspielman in #859
• Updated wilms clustering notebooks 1/3 by @sjspielman in #862
• Updated wilms clustering notebooks 2/3 by @sjspielman in #863
• Updated wilms clustering notebooks 3/3 by @sjspielman in #864
• Wilms 06 module: Update and re-render 04 notebook by @sjspielman in #867
• Use docker image for wilms-14 CI by @jashapiro in #842
• Add dockerfile for metacell analysis by @jashapiro in #869
• Wilms-06 update CNV methods: copykat (1/3) by @sjspielman in #872
• Wilms-06 update CNV methods: infercnv (2/3) by @sjspielman in #873
• Update calculate_stability usage by @sjspielman in #871
• Update simulate-sce to keep all metadata columns by @jashapiro in #879
• Account for multiplexed samples in metadata permutation by @jashapiro in #880
• Wilms-06 update CNV methods (3/3), and run module in CI by @sjspielman in #876
• Add rOpenScPCA to renv/docker in ewing module by @allyhawkins in #881
• Fix wilms-06 typos by @sjspielman in #885
• Add zellkonverter to wilms-06 environment by @sjspielman in #890
• Merge main into feature/wilms-tumor-06-azimuth by @sjspielman in #891
• Merge wilms-tumor-06-azimuth into main by @sjspielman in #893
• Remove zero cells in simulations by @jashapiro in #898
• only warn if there are too many labels in simulations by @jashapiro in #901
• Initiate module for consensus cell typing by @allyhawkins in #903
• Update creating-vcs.md to no longer reference selecting an Availability Zone by @jaclyn-taroni in #904
• Use h5ad reference in cell-type-wilms-tumor-06 by @sjspielman in #902
• Update clustering report to include leiden clustering by @allyhawkins in #895
• Shrink and fix simulated SCEs by @jashapiro in #907
• Fix spelling errors by @sjspielman in #911
• Add workflow for evaluating clustering to Ewing's module by @allyhawkins in #908
• Initial assignment of cell ontology IDs to panglao cell types by @allyhawkins in #909
• Regenerate wilms notebooks: Code updates by @sjspielman in #913
• Regenerate wilms-tumor-06 notebooks 2/N by @sjspielman in #916
• Wilms tumor notebooks: next batch by @sjspielman in #918
• Make sure cluster assignments are factors by @allyhawkins in #919
• Next batch of SCPCP000006 notebooks by @sjspielman in #921
• Penultimate batch of SCPCP000006 notebooks by @sjspielman in #922
• Last batch of SCPCP000006 notebooks by @sjspielman in #923
• Second group of manual cell type ontology assignments by @allyhawkins in #917
• Add first set of manual cell ontology assignments by @allyhawkins in #914
• Specify number of threads used when calculating cluster stability by @allyhawkins in #925

Full Changelog: 2024-11-07...2024-12-03