kleinstein / shazam / issues

Title	T	P	Status	Assignee	Created	Updated
#102: findThreshold seems to be stuck forever	bug	major	resolved	nima nouri	2018-01-09	2018-02-15
#103: calculateTargeting fails due to gaps in subSeq	bug	major	resolved		2018-02-05	2018-02-05
#100: observedMutations breaking with additional columns	bug	major	wontfix	Jason Vander Heiden	2017-10-12	2017-10-13
#98: Baseline Statistics Outputting Same FDR	bug	critical	resolved	Jason Vander Heiden	2017-10-12	2017-10-12
#96: shmulateSeq() breaks when there's gap in input sequence	bug	major	resolved		2017-08-10	2017-08-10
#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
#94: Error in createMutationDefinition examples	bug	minor	resolved	Jason Vander Heiden	2017-06-09	2017-06-12
#92: add tests for calcClonalConsensus and collapseClones	task	critical	resolved	Julian Zhou	2017-06-02	2017-06-12
#87: Column names for mutation counts and frequencies are inconsistent	enhancement	minor	resolved		2017-05-12	2017-06-09
#85: distToNearest failed in sbatch mode on Farnam	bug	minor	resolved		2017-05-10	2017-06-09
#91: add option to break ties using additional columns (only if it's not too much work)	enhancement	trivial	resolved	Julian Zhou	2017-06-02	2017-06-09
#90: bring back stochastic option for calcClonalConsensus	enhancement	minor	resolved	Julian Zhou	2017-06-02	2017-06-09
#89: create most/least mutated seq option for calcClonalConsensus	enhancement	minor	resolved	Julian Zhou	2017-06-02	2017-06-09
#93: adapt calcObservedMutations for seq containing ambiguous character	task	major	resolved	Julian Zhou	2017-06-02	2017-06-07
#56: Add unique mutations per clone measures to targeting model generation	enhancement	major	wontfix	Julian Zhou	2016-05-10	2017-06-02
#27: Add options to clonal consensus generation to create non-randomized consensus sequences	enhancement	major	resolved	Julian Zhou	2015-06-19	2017-06-02
#86: distToNeareast failed on local machine too	bug	major	resolved		2017-05-11	2017-05-12
#82: dply 0.6.0 incompatibility	bug	minor	resolved	Jason Vander Heiden	2017-04-25	2017-05-05
#66: swap ape::mst for igraph::mst	enhancement	minor	wontfix	Namita Gupta	2016-07-29	2017-03-23
#69: findthreshold()	enhancement	major	resolved	sivagnon@gmail.com	2016-10-31	2017-03-23
#75: findThreshold is slow	enhancement	major	resolved	nima nouri	2016-11-25	2017-03-23
#80: non-NA sigma mean returned by BASELINe local test for codons with no sequence data during codon-by-codon analysis	bug	major	resolved	Julian Zhou	2017-03-08	2017-03-08
#79: In collapseClones and DistToNearest foreach implementation is suppressing errors	bug	minor	resolved	ssnn	2017-01-25	2017-02-27
#78: Non-existent regionDefinition fails to produce sensible error	bug	minor	resolved		2017-01-24	2017-01-25