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
lengthfornrowby @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 testrun_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