v1.1.1

What's Changed

• Basic infrastructure: Add Dockerfile and basic testing for this repository by @cansavvy in #8
• Setting up data for analysis!! by @cansavvy in #12
• added todo comments for clarification by @danieljgroso in #15
• DRAFT: Polishing Ideas for QC code by @cansavvy in #17
• fix cpm calculations by @kweav in #20
• Quality Control -- Report Making Function by @kweav in #16
• Feedback on Getting Started Vignette by @howardbaik in #18
• gimap suggested structure and schema by @cansavvy in #22
• fix nrow to ncol by @kweav in #27
• Update 00-setup_data.R to switch ncol to nrow by @kweav in #29
• Update 00-setup_data.R to switch length for nrow by @kweav in #30
• first commit - QC vignette description, getting_started.Rmd by @danieljgroso in #23
• scratch code ki for replicate variation filter by @kweav in #31
• add file showing code for review by @kweav in #32
• Annotation schema by @cansavvy in #25
• update QC report with two graphs by @kweav in #33
• split up filters from plots and add tables to report by @kweav in #34
• Start with adding parameters that allow the user to select which column(s) are used in various filtering or filtering-related visualization steps by @kweav in #35
• Fix setup_data() by @howardbaik in #37
• Add ability to select columns for the zerocount filter by @kweav in #38
• Add ability to select columns for the last sample replicates by @kweav in #39
• Beginning of making filtering steps all work together by @kweav in #41
• Filtering step runs and stores result by @kweav in #40
• start recording extra info on pg IDs by @kweav in #43
• Annotation Review after Filtering by @kweav in #44
• Fix bugs in run_qc()and test run_qc() by @howardbaik in #45
• Test setup_data() by @howardbaik in #42
• Log fold change by @cansavvy in #26
• Docker updates by @cansavvy in #47
• Genetic Interaction Step by @cansavvy in #36
• Some comparisons of the LFC results between GI Mapping and gimap by @kweav in #49
• Update docs by @cansavvy in #51
• review of first CRISPR score calculation by @kweav in #52
• add beginning of GI review by @kweav in #53
• Adjust code, headers, and vignette for required/not required arguments by @kweav in #56
• cell_line needs to be specified by @cansavvy in #57
• Specify fastmap version in DESCRIPTION by @kweav in #61
• add filtering by @kweav in #62
• Making this work for different experimental set ups by @cansavvy in #63
• Make depmap annotation optional by @cansavvy in #65
• comparison of new and old results by @kweav in #64
• Add readability report by @cansavvy in #70
• Update gi handling scores by @cansavvy in #68
• New documentation to make it clearer! by @cansavvy in #73
• We want mean_observed_cs saved too by @cansavvy in #75
• Adding tests by @cansavvy in #76
• Experimenting with CRISPR calculations by @cansavvy in #77
• Added support for main plots by @kweav in #71
• slight edits to headers by @kweav in #80
• Custom TPM argument by @cansavvy in #79
• Getting this CRAN ready by @cansavvy in #82
• Use zip or download strategy by @cansavvy in #83
• Figshare Auth by @cansavvy in #84
• QC fix by @cansavvy in #85
• Put more data on figshare by @cansavvy in #86
• Turn off vignettes so its faster for CRAN by @cansavvy in #87
• Fix bar plot to be the mean by @cansavvy in #88
• Addressing CRAN review comments by @cansavvy in #89
• CRAN review updates part 3 by @cansavvy in #90
• Downloads aren't working - wget in particular by @cansavvy in #91
• Fix bug with using custom annotation file by @marissafujimoto in #93
• Rep collapse option by @cansavvy in #94
• Updates to CRAN by @cansavvy in #95
• Do mean GIs as baseline by @cansavvy in #97
• CRAN update by @cansavvy in #99
• SUPER drafty Paper 💨 by @cansavvy in #98
• Update paper.md by @ahberger in #103
• Paper Draft! by @cansavvy in #100

New Contributors

• @cansavvy made their first contribution in #8
• @danieljgroso made their first contribution in #15
• @kweav made their first contribution in #20
• @howardbaik made their first contribution in #18
• @marissafujimoto made their first contribution in #93

Full Changelog: https://github.com/FredHutch/gimap/commits/v1.1.1