kleinstein / shazam / issues

Title	T	P	Status	Assignee	Created	Updated
#165: Possible misuse of `all.equal` in the definition of `observedMutations`	bug	minor	resolved		2023-11-01	2023-11-06
#160: Weighted collapseClones mostcommon	enhancement	minor	new		2022-02-23	2022-02-23
#157: MMR in SHmulate	proposal	minor	resolved		2021-09-30	2021-10-14
#156: collapseClones unused argument "fields"	bug	minor	resolved		2021-09-22	2021-09-23
#153: Add an option to `observedMutations` to always report stop mutations	proposal	minor	new		2021-07-08	2021-07-08
#147: Validate sequences before counting mutations	enhancement	minor	new		2020-10-29	2020-10-29
#118: Improve docs	enhancement	minor	open	ssnn	2019-01-25	2020-10-26
#132: distToNearest won't work if V_CALL or J_CALL are factors	bug	minor	resolved		2020-04-22	2020-04-29
#111: Improve performance of observedMutations	enhancement	minor	on hold	Roy Jiang	2018-07-13	2020-04-03
#129: Add number of mutations used for building targeting models in output	enhancement	minor	resolved	Julian Zhou	2020-03-06	2020-03-23
#119: Add to shmulateSeq option to specify mutations in percent	proposal	minor	resolved	Julian Zhou	2019-01-25	2020-03-23
#107: density method of findThreshold might need a bandwidth adjustment	enhancement	minor	resolved	nima nouri	2018-05-24	2018-09-14
#112: Grouping section of the selection vignette is unclear	enhancement	minor	resolved		2018-07-31	2018-08-27
#110: Add subsampling to distToNearest	enhancement	minor	resolved	nima nouri	2018-07-03	2018-08-02
#101: create shazam::indexByUnion	proposal	minor	resolved	nima nouri	2017-12-08	2018-07-16
#108: Edit help text to make clear when some codons are excluded by observedMutations	task	minor	resolved	Julian Zhou	2018-05-31	2018-05-31
#97: Write test for distToNearest when seq has stop codon	enhancement	minor	resolved	nima nouri	2017-09-21	2018-03-29
#64: Mutation profiling and shmulate vignette	enhancement	minor	resolved	Julian Zhou	2016-07-17	2018-03-16
#12: Add way to highlight specific 5-mers in mutability plots	enhancement	minor	resolved	Jason Vander Heiden	2015-05-06	2018-03-14
#105: Add dispatch to plot for Baseline and TargetingModel objects	enhancement	minor	resolved		2018-02-26	2018-03-14
#52: Add RegionDefinition for full V-region	enhancement	minor	resolved		2016-02-19	2018-03-14
#6: Could use plotting functions for substitution and targeting	enhancement	minor	wontfix	Jason Vander Heiden	2015-05-01	2018-03-14
#4: Add method to subset Baseline objects	enhancement	minor	wontfix	Mohamed Uduman	2015-05-01	2018-03-14
#88: Fix calcBaseline for data.frame and tbl	bug	minor	resolved	ssnn	2017-05-20	2017-06-15
#95: User-defined sensitivity or specificity for gmm cutoff choice	enhancement	minor	resolved	nima nouri	2017-06-12	2017-06-13