SPEEDI v1.2.1: Bug Fixes for ATAC Processing

Small updates to fix ATAC processing.

SPEEDI v1.2.0: Updates to Support Seurat V5 Changes

Updated SPEEDI to support changes in Seurat V5.

Other minor changes:

1. Users can set resolution parameter in VisualizeIntegration() function.
2. Downstream analysis is now robust against failed POST calls in functional module discovery (will exit cleanly).
3. Renamed data_path to input_dir.

SPEEDI v1.1.4: SPEEDI RDS File Save Bug Fix

Minor bug fix when saving RDS file from SPEEDI RNA analysis (now uses saveRDS() instead of just save()).

SPEEDI v1.1.3: HumanBase Functional Module Discovery Bug Fix

Bug fix for functional module discovery (genes with hyphens in name were being incorrectly matched in the HB database). These genes are now ignored for FMD.

SPEEDI v1.1.2: ATAC Cell Type Integration Fix

Small bug fix for ATAC cell type integration (now uses correct dimensions)

SPEEDI v1.1.1: Batch Inference Bug Fix

Fixed bug related to batch inference for ATAC data

SPEEDI v1.1.0: Batch Inference Update

We have updated the data-derived batch inference method to be more robust to randomness and more accurate.

Official Release of SPEEDI

v1.0.0

WT: Updated version for release