Liulab Dfci MAESTRO Versions Save

• Expand STARsolo --soloFeatures and --runThreadN as MAESTRO subcommands.
• Support single-nuclei RNA-seq pipeline.
• Fix bug in sample initiation subcommand to read fastq with sample id greater than 9.
• Update MAESTRO documentation to v1.5.1. Add snRNA-seq tutorials. Expand scRNA-seq tutorial with lisa2 TF prediction custom analysis.
• Add multi-scATAC-seq genome track plot for pseudobulk peaks. Explain multi-samples peak calling parameters.

v1.5.0

• Support processing multi-samples for both scRNA-seq and scATAC-seq.
• Support multi-sample scATAC-seq when starting from bam file with CB tag or 10X like fragment file.
• Fix the ratio of genes mapped to mitochondrial to percentage.
• Move MAESTRO documentation to workfowr.

1. Upgrade R package dependencies to Seurat4.0.0 and Signac1.1.1.
2. Move functions from the old Seurat package to Signic.
3. Fix mito.cutoff rate as a variable.
4. Add output directory option in MAESTRO R package.

• Move from TravisCI to GitHub Actions for building package.
• LISA2 upgrades to v2.2.2. New LISA data are required for human and mouse. Please download to your computer and provide the path when initiating.
• Add LISA path as a variable in TF annotating function.
• Reduce the time and memory usage in the peak counting step.
• Fix a bug in the simple RP model for gene score calculation.
• Fix a bug in scATAC-Seq Snakefile.

• fix a bug when generating raw scATAC-seq count matrix. Do not count duplicates within a cell.

• scATAC-seq multi-sample pipeline enabled. Deduplication can be set at the cell or bulk level.
• Peak count matrix can be generated either as a binary or raw count matrix.
• LISA2 data will only be configured once in a given environment.
• Update web links for downloading reference data.

• Update LISA to LISA2 which extends the original, runs faster, reduces dependencies, and adds useful CLI functions for pipeline integration. Please download the LISA2 data from human and mouse.
• Update conda dependencies to only requesting lowest versions.
• Fix the bugs in conda package installation channel.
• Update markers in the mouse.brain.ALLEN cell signature file.
• Fix the bugs to support the 10X .h5 file as the input format of MAESTRO scatac-genescore.
• Rename 'Adjusted RP model' to 'Enhanced RP model'.
• Fix the bugs in Snakefile to meet the latest version of snakemake.
• Update STAR reference indexes files for STAR -version 2.7.6a. Provide pre-built indexes for human and mouse.

v1.2.1.999, a beta release for v1.2.2 (bug fixes)

• gene score calculation
• mouse brain ALLEN signatures
• memory issue when merging h5 file
• etc

• For scATAC, support fastq, bam, fragments.tsv.gz as the input of the scATAC-seq workflow;
• For scATAC, provide an option for users to skip the cell-type annotation step in the pipeline, and an option to choose the strategy for cell-type annotation (ATACAnnotateCelltype and ATACAnnotateChromatinAccessibility);
• Provide small test data for test scRNA-seq and scATAC-seq pipeline (sampling from 10x fastq files);
• Add parameter validation before initializing the pipeline and provide more gracious error messages;
• Update R in MAESTRO conda package to 4.0.2, and Seurat to 3.1.5

MAESTRO v1.1.0