First Release

Initial release of GAMBLR with bundled data (via GAMBLR.data).

What's Changed

• Adding some bed files by @lkhilton in #2
• add CN for unmatched samples by @Kdreval in #3
• minor updates to annotate_hotspots by @Kdreval in #4
• add functionality to allow non-morinlab group members to use GAMBLR a… by @rdmorin in #5
• update prettyOncoplot to work with new ggsci colours by @rdmorin in #6
• add p_val threshold to arguments by @rdmorin in #7
• updates to using bundled colours for GAMBL metadata by @rdmorin in #8
• Kdreval unmatched cn by @Kdreval in #9
• fix bug in prettyOncoplot by @rdmorin in #10
• introduce prettyChromoplot to handle GISTIC scores by @Kdreval in #11
• some bug fixes and new features plus a presentation by @rdmorin in #13
• extend ashm_matrix code to work without database by @rdmorin in #14
• suppress obnoxious messages by @rdmorin in #15
• Bug fix and minor improvements by @rdmorin in #16
• introduce function for Fisher's exact test of GISTIC2.0 outputs by @Kdreval in #12
• bug fix by @rdmorin in #17
• finally fix all commonly conflicted dplyr function calls by @rdmorin in #18
• new and updated functions by @rdmorin in #20
• Rmorin dev by @rdmorin in #21
• new functionality for working with merged flatfiles and non-ICGC data by @rdmorin in #22
• support custom colors in prettyOncoplot annotations by @Kdreval in #23
• updates to shm analyses by @rdmorin in #24
• some minor updates to aSHM code by @rdmorin in #26
• bug fixes by @rdmorin in #27
• adult BL paper and FL+all DLBCL case sets by @Kdreval in #25
• add missing data and some bug fix by @rdmorin in #28
• Customize get_mutation_frequency_bin_matrix by @Kdreval in #29
• More from-flatfile functionality to reduce reliance on the database by @rdmorin in #30
• new functions and some bug fixes by @Kdreval in #31
• some updates by @rdmorin in #32
• Fixed bug enabling top barplot by @kristenadaley in #33
• update function to accept maf and seg file paths by @kristenadaley in #34
• update to case sets by @rdmorin in #35
• fix FL cohort and use transformation status for tFL-study case set by @rdmorin in #36
• prettyForestPlot by @lkhilton in #37
• add purity estimate function and adjust assign_cn_to_ssm function to … by @kristenadaley in #39
• Rmorin dev by @rdmorin in #38
• added packages in the @input section for purity estimation function by @kristenadaley in #40
• improved and possibly broke prettyForestPlot by @rdmorin in #42
• estimate_purity function modifications by @kristenadaley in #43
• modified how plots and tables are output from the estimate_purity fun… by @kristenadaley in #44
• Rmorin dev by @rdmorin in #45
• do you like Heatmap function name? by @Kdreval in #41
• add function for gridss svs by @rdmorin in #47
• Lhilton tidy inputs by @lkhilton in #49
• switch ssm results from current to versioned results by @Kdreval in #46
• Kdreval dev by @Kdreval in #59
• Update to handle capture data by @rdmorin in #60
• Add a function to tidy LymphGen Subtype.Prediction columns by @lkhilton in #63
• changed final purity above 1 to equal 1 and fix some bugs in purity e… by @kristenadaley in #61
• GAMBLR Code Review by @mattssca in #53
• fixing typo that broke GAMBLR install by @mattssca in #65
• Functionality to prepare matrix for NMF clustering + bug fixes by @Kdreval in #68
• add rainfall plot basic functionality by @rdmorin in #69
• Updates to the prettyRainfallPlot by @Kdreval in #70
• fix broken get_gambl_metadata function by @rdmorin in #72
• updating ssm functions to read from latest deblacklsited maf by @mattssca in #71
• New functions: calculate PGA and adjust ploidy by @Kdreval in #73
• Bug fix: positional arguments in get_ssm_by_samples call to get_ssm_b… by @lkhilton in #84
• Implement flatfile functionality for CNV and introduce cnvKompare by @Kdreval in #86
• plot updates, vignette & bug fixes, etc. by @mattssca in #85
• fix flatfile reading in get_manta_sv by @rdmorin in #82
• Fix duplicated argument by @rdmorin in #90
• Bug fixes, new plotting functions, vignette examples, etc. by @mattssca in #88
• init prettyCoOncoplot by @Kdreval in #92
• add cohort colours and fix MZL by @rdmorin in #93
• update collate functions to work for genome and capture data by @rdmorin in #96
• Kdreval dev by @Kdreval in #101
• Cmattsson dev by @mattssca in #91
• Remote GAMBLR (outside GSC) is now a thing. Testers wanted! by @rdmorin in #99
• fix new bugs associated with ssh_session by @rdmorin in #107
• hot-fix for get_ssm_by_region (and added plotting functions) by @mattssca in #108
• Updated README with instructions on how to run run GAMBLR remote + other QoL updates (messages, warnings etc.) by @mattssca in #109
• new feature: right annotations in prettyOncoplot by @Kdreval in #103
• New plotting functions and various improvements. by @mattssca in #110
• Revert "new line" by @rdmorin in #111
• New RF, new function, update to splendidHeatmap, and bug fixes by @Kdreval in #116
• Fancy Plots + QoL Updates by @mattssca in #115
• add sample set md5 digest functionality for reproducibility by @rdmorin in #114
• Fix LymphGen tidy class order by @lkhilton in #122
• Bug fix: bam_available wasn't being filtered on conditionally by @lkhilton in #124
• Do-over of last PR by @rdmorin in #130
• update estimate_purity function to set the assume_diploid parameter t… by @kristenadaley in #119
• Adding error messages to functions that reads from local files. by @mattssca in #117
• collate_results fix by @mattssca in #133
• Add additional blacklist to annotate_ssm_blacklist() by @hayashaalan in #104
• GAMBLR OveRhaul by @rdmorin in #137
• GAMBLR hotfixes and improvements. by @mattssca in #142
• classify FLs functionality + bug fix by @Kdreval in #141
• GAMBLR Improvements by @mattssca in #148
• Adding packages to and tidy DESCRIPTION file + hotfix for get manta_sv_by_sample by @mattssca in #152
• prettyOncoplot updated to be able to handle input genes and minMutationPercent by @faranehym in #165
• Resolving issues, bugs, and making reproducible installation by @Kdreval in #146
• Add new functions for loading Manta SV from individual files instead of merges by @rdmorin in #143
• bug fix: prettyForestplot bugs by @Kdreval in #167
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