NEWS.md

In openCyto: Hierarchical Gating Pipeline for flow cytometry data

openCyto 1.3.17

Enhancements

• more robust csv parsing
• register wrapper function for quadGate.seq
• parse 'subSample' argument from 'gating_args' column in csv template to allow subsampling the data prior to gating.
• pass ... from quantileGate to quantile function
• add method for multipleFitlerResult
• support multi-dimensions in framework by deprecating x,y with channels.

Bug Fixes:

• fix the bug that stop.at argument to gating doesn't recognize partial or full path

openCyto 1.7.1

Enhancements

• New API: add_pop function allows users to apply a single gating method to GatingSet without writing the compelete csv template

openCyto 1.23.5 (Bioconductor version 3.10)

API Changes

Simple renaming

• gate_flowClust_1d -> gate_flowclust_1d
• gate_flowClust_2d -> gate_flowclust_2d
• tautStringGate -> gate_tautstring
• templateGen -> gh_generate_template
• add_pop_init -> gs_add_gating_method_init
• add_pop -> gs_add_gating_method
• remove_pop -> gs_remove_gating_method
• get.helperGates -> gs_get_helpergates
• toggle.helperGates -> gt_toggle_helpergates
• delete.helperGates -> gs_delete_helpergates
• getNodes -> gt_get_nodes
• getParent -> gt_get_parent
• getChildren -> gt_get_children
• getGate -> gt_get_gate
• gating -> gt_gating
• registerPlugins -> register_plugins

Classes and methods no longer exported

• registerGatingFunction
• gtMethod
• gtPopulation
• polyFunctions
• ppMethod

Bug Fixes

• Some minor fixes to gt_toggle_helpergates
• Fix "positive" argument to gate_mindensity to match doc

openCyto 1.25.x (Bioconductor version 3.11)

Enhancements

• Allow control of mininum number of events for each step of GatingTemplate #298

Bug Fixes

• Handle a few more edge cases in .improvedMinDensity
• Added a fix to the density estimate used by gate_tautstring

openCyto documentation built on Nov. 8, 2020, 5:40 p.m.