CHANGES.md

Changes

1.3.7

• Update RCRISPR to 1.2.2.0 (allows numeric sample names in count and fold change matrices)

1.3.6

• Update BAGEL config scaled_bf_infile_gene_column_index to 2

1.3.5

• Requires RCRISPR >= 1.2.1.0
• Allow QC PCA plots to use shape when groups not enabled
• Use BAGEL sgRNA BF file to calculate gene-level BFs (average of sgRNA BFs per gene)

1.3.4

Add contrast (e.g. treatment_vs_plasmid) and input type (e.g. counts or fc) to filename suffix for intermediate QC BAGEL statistics files.

• With NNMD (gene level fold changes): bagel_classification_summary.treatment_vs_plasmid.fc.tsv
• Without NNMD (sgrna counts): bagel_classification_summary.treatment_vs_plasmid.counts.tsv

1.3.3

RRA processing enriched/depleted files optional for MAGeCK

1.3.2

Update RCRISPR to 1.1.1.0

1.3.1

Teething issue with first tagged CI build

1.3.0

First public release. Linked to RCRISPR 1.1.0.0.

1.2.0

• Update functions for nnmd and glass delta
• Round glass and nnmd to 3dp
• Update to ubuntu:20.04 due to R issues
  • Additionally improve R package installs by adding versions