{ "_id": "6a1f0755b401979e7341beb1", "Package": "HaploVar", "Type": "Package", "Title": "Defining Local Haplotype Variants for Use in Trait Association\nand Trait Prediction Analyses", "Version": "0.1.1", "Authors@R": "c(person(\"Tessa\", \"MacNish\", email = \"tessa.macnish@research.uwa.edu.au\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0009-0008-8985-7348\")), person(\"Hawlader\", \"Al-Mamun\", role = \"ctb\"), person(\"Thomas\", \"Bergmann\", role = \"ctb\"), person(\"Mitchell\", \"Bestry\", role = \"ctb\"), person(\"Jacob\", \"Marsh\", role = \"ctb\"), person(\"David\", \"Edwards\", role = \"ctb\"))", "Description": "A local haplotyping tool for use in trait association and\ntrait prediction analyses pipelines. 'HaploVar' enables users\ntake single nucleotide polymorphisms (SNPs) (in VCF format) and\na linkage disequilibrium (LD) matrix, calculate local\nhaplotypes and format the output to be compatible with a wide\nrange of trait association and trait prediction tools. The\nlocal haplotypes are calculated from the LD matrix using a\nclustering algorithm called density-based spatial clustering of\napplications with noise ('DBSCAN') (Ester et al., 1996) .", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "RoxygenNote": "7.3.2", "LazyData": "true", "LazyDataCompression": "xz", "VignetteBuilder": "knitr", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-18 06:48:51 UTC", "User": "root" }, "Author": "Tessa MacNish [aut, cre] (ORCID:\n), Hawlader Al-Mamun\n[ctb], Thomas Bergmann [ctb], Mitchell Bestry [ctb], Jacob\nMarsh [ctb], David Edwards [ctb]", "Maintainer": "Tessa MacNish ", "Config/pak/sysreqs": "libicu-dev", "Repository": "https://t-macnish.r-universe.dev", "Date/Publication": "2025-07-21 08:31:11 UTC", "RemoteUrl": "https://github.com/cran/HaploVar", "RemoteRef": "HEAD", "RemoteSha": "7402a12912cb4ebd15ba168e748b2eb3c1f30722", "MD5sum": "e0b9d4e4117f4dfb8f54b60e423d0289", "_user": "t-macnish", "_type": "src", "_file": 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"R4350_R4350", "R4351_R4351", "R4352_R4352", "R4353_R4353", "R4354_R4354", "R4355_R4355", "R4356_R4356", "R4357_R4357", "R4358_R4358", "R4359_R4359", "R4360_R4360", "R4361_R4361", "R4363_R4363", "R4364_R4364", "R4365_R4365", "R4366_R4366", "R4367_R4367", "R4368_R4368", "R4369_R4369", "R4370_R4370", "R4371_R4371", "R4372_R4372", "R4373_R4373", "R4374_R4374", "R4375_R4375", "R4376_R4376", "R4377_R4377", "R4378_R4378", "R4379_R4379", "R4380_R4380", "R4381_R4381", "R4382_R4382", "R4383_R4383", "R4384_R4384", "R4385_R4385", "R4386_R4386", "R4387_R4387", "R4388_R4388", "R4389_R4389", "R4390_R4390", "R4391_R4391", "R4392_R4392", "R4393_R4393", "R4395_R4395", "R4396_R4396", "R4397_R4397", "R4398_R4398", "R4399_R4399", "R4400_R4400", "R4401_R4401", "R4402_R4402", "R4403_R4403", "R4404_R4404", "R4405_R4405", "R4406_R4406", "R4407_R4407", "R4408_R4408", "R4409_R4409", "R4410_R4410", "R4411_R4411", "R4412_R4412", "R4413_R4413", "R4414_R4414", "R4415_R4415", "R4416_R4416", "R4417_R4417", "R4418_R4418", "R4419_R4419", "R4420_R4420", "R4421_R4421", "R4422_R4422", "R4423_R4423", "R4424_R4424", "R4425_R4425", "R4426_R4426", "R4427_R4427", "R4428_R4428", "R4429_R4429", "R4430_R4430", "R4431_R4431", "R4432_R4432", "R4433_R4433", "R4434_R4434", "R4435_R4435", "R4436_R4436", "R4437_R4437", "R4438_R4438", "R4439_R4439", "R4440_R4440", "R4441_R4441", "R4442_R4442", "R4443_R4443", "R4444_R4444", "R4445_R4445", "R4446_R4446", "R4447_R4447", "R4448_R4448", "R4449_R4449", "R4450_R4450", "R4451_R4451", "R4452_R4452", "R4453_R4453", "R4454_R4454", "R4455_R4455", "R4456_R4456", "R4457_R4457", "R4458_R4458", "R4459_R4459", "R4460_R4460", "R4461_R4461", "R4462_R4462", "R4463_R4463", "R4464_R4464", "R4465_R4465", "R4466_R4466", "R4467_R4467", "R4468_R4468", "R4469_R4469", "R4470_R4470", "R4471_R4471", "R4472_R4472", "R4473_R4473", "R4474_R4474", "R4476_R4476", "R4477_R4477", "R4478_R4478", "R4479_R4479", "R4480_R4480", "R4481_R4481", "R4482_R4482", "R4483_R4483", "R4484_R4484", "R4485_R4485", "R4486_R4486", "R4487_R4487", "R4488_R4488", "R4489_R4489", "R4491_R4491", "R4492_R4492", "R4493_R4493", "R4494_R4494", "R4495_R4495", "R4496_R4496", "R4497_R4497", "R4498_R4498", "R4500_R4500", "R4501_R4501", "R4502_R4502", "R4503_R4503", "R4504_R4504", "R4506_R4506", "R4507_R4507", "R4508_R4508", "R4509_R4509", "R4510_R4510", "R4511_R4511", "R4512_R4512", "R4513_R4513", "R4514_R4514", "R4515_R4515", "R4516_R4516", "R4517_R4517", "R4518_R4518", "R4519_R4519", "R4520_R4520", "R4521_R4521", "R4522_R4522", "R4523_R4523", "R4524_R4524", "R4525_R4525", "R4526_R4526", "R4527_R4527", "R4528_R4528", "R4529_R4529", "R4531_R4531", "R4532_R4532", "R4533_R4533", "R4534_R4534", "R4535_R4535", "R4536_R4536", "R4537_R4537", "R4538_R4538", "R4539_R4539", "R4540_R4540", "R4541_R4541", "R4542_R4542", "R4543_R4543", "R4544_R4544", "R4545_R4545", "R4546_R4546", "R4547_R4547", "R4548_R4548", "R4549_R4549", "R4550_R4550", "R4551_R4551", "R4552_R4552", "R4553_R4553", "R4554_R4554", "R4555_R4555", "R4556_R4556", "R4557_R4557", "R4558_R4558", "R4559_R4559", "R4560_R4560", "R4561_R4561", "R4562_R4562", "R4563_R4563", "R4564_R4564", "R4565_R4565", "R4566_R4566", "R4567_R4567", "R4568_R4568", "R4569_R4569", "R4570_R4570", "R4571_R4571", "R4572_R4572", "R4573_R4573", "R4574_R4574", "R4575_R4575", "R4576_R4576", "R4577_R4577", "R4578_R4578", "R4579_R4579", "R4580_R4580", "R4581_R4581", "R4582_R4582", "R4583_R4583", "R4584_R4584", "R4585_R4585", "R4586_R4586", "R4587_R4587", "R4588_R4588", "R4589_R4589", "R4590_R4590", "R4591_R4591", "R4592_R4592", "R4593_R4593", "R4594_R4594", "R4595_R4595", "R4596_R4596", "R4597_R4597", "R4598_R4598", "R4599_R4599", "R4600_R4600", "R4601_R4601", "R4602_R4602", "R4603_R4603", "R4604_R4604", "R4605_R4605", "R4606_R4606", "R4607_R4607", "R4608_R4608", "R4609_R4609", "R4610_R4610", "R4611_R4611", "R4612_R4612", "R4613_R4613", "R4614_R4614", "R4615_R4615", "R4616_R4616", "R4617_R4617", "R4618_R4618", "R4619_R4619", "R4620_R4620", "R4621_R4621", "R4622_R4622", "R4623_R4623", "R4624_R4624", "R4625_R4625", "R4626_R4626", "R4627_R4627", "R4628_R4628", "R4629_R4629", "R4630_R4630", "R4631_R4631", "R4632_R4632", "R4633_R4633", "R4634_R4634", "R4635_R4635", "R4636_R4636", "R4637_R4637", "R4638_R4638", "R4639_R4639", "R4640_R4640", "R4641_R4641", "R4642_R4642", "R4643_R4643", "R4644_R4644", "R4645_R4645", "R4646_R4646", "R4647_R4647", "R4648_R4648", "R4649_R4649", "R4650_R4650", "R4651_R4651", "R4652_R4652", "R4653_R4653", "R4654_R4654", "R4655_R4655", "R4656_R4656", "R4657_R4657", "R4658_R4658", "R4659_R4659", "R4660_R4660", "R4661_R4661", "R4662_R4662", "R4663_R4663", "R4664_R4664", "R4665_R4665", "R4666_R4666", "R4667_R4667", "R4668_R4668", "R4669_R4669", "R4670_R4670", "R4671_R4671", "R4672_R4672", "R4673_R4673", "R4674_R4674", "R4675_R4675", "R4676_R4676", "R4677_R4677", "R4678_R4678", "R4679_R4679", "R4680_R4680", "R4681_R4681", "R4682_R4682", "R4683_R4683", "R4684_R4684", "R4685_R4685", "R4686_R4686", "R4687_R4687", "R4688_R4688", "R4689_R4689", "R4690_R4690", "R4691_R4691", "R4692_R4692", "R4693_R4693", "R4694_R4694", "R4695_R4695", "R4696_R4696", "R4697_R4697", "R4698_R4698", "R4699_R4699", "R4700_R4700", "R4701_R4701", "R4702_R4702", "R4703_R4703", "R4704_R4704", "R4705_R4705", "R4706_R4706", "R4707_R4707", "R4708_R4708", "R4709_R4709", "R4710_R4710", "R4711_R4711", "R4712_R4712", "R4713_R4713", "R4714_R4714", "R4715_R4715", "R4716_R4716", "R4717_R4717", "R4718_R4718", "R4719_R4719", "R4720_R4720", "R4721_R4721", "R4722_R4722", "R4723_R4723", "R4724_R4724", "R4725_R4725", "R4726_R4726", "R4727_R4727", "R4728_R4728", "R4729_R4729", "R4730_R4730", "R4731_R4731", "R4732_R4732", "R4733_R4733", "R4734_R4734", "R4735_R4735", "R4736_R4736", "R4737_R4737", "R4738_R4738", "R4739_R4739", "R4740_R4740", "R4741_R4741", "R4742_R4742", "R4743_R4743", "R4744_R4744", "R4745_R4745", "R4746_R4746", "R4747_R4747", "R4748_R4748", "R4749_R4749", "R4750_R4750", "R4751_R4751", "R4752_R4752", "R4753_R4753", "R4754_R4754", "R4755_R4755", "R4756_R4756", "R4757_R4757", "R4758_R4758", "R4759_R4759", "R4760_R4760", "R4761_R4761", "R4762_R4762", "R4763_R4763", "R4765_R4765", "R4766_R4766", "R4767_R4767", "R4768_R4768", "R4769_R4769", "R4770_R4770", "R4771_R4771", "R4772_R4772", "R4773_R4773", "R4774_R4774", "R4775_R4775", "R4776_R4776", "R4777_R4777", "R4778_R4778", "R4779_R4779", "R4780_R4780", "R4781_R4781", "R4782_R4782", "R4783_R4783", "R4784_R4784", "R4785_R4785", "R4786_R4786", "R4787_R4787", "R4788_R4788", "R4789_R4789", "R4790_R4790", "R4791_R4791", "R4792_R4792", "R4793_R4793", "R4794_R4794", "R4795_R4795", "R4796_R4796", "R4797_R4797", "R4798_R4798", "R4799_R4799", "R4800_R4800", "R4801_R4801", "R4802_R4802", "R4803_R4803", "R4804_R4804", "R4805_R4805", "R4806_R4806", "R4807_R4807", "R4808_R4808", "R4809_R4809", "R4810_R4810", "R4811_R4811", "R4812_R4812", "R4813_R4813", "R4814_R4814", "R4815_R4815", "R4816_R4816", "R4817_R4817", "R4818_R4818", "R4819_R4819", "R4820_R4820", "R4821_R4821", "R4822_R4822", "R4823_R4823", "R4824_R4824", "R4825_R4825", "R4826_R4826", "R4827_R4827", "R4828_R4828", "R4829_R4829", "R4830_R4830", "R4831_R4831", "R4832_R4832", "R4833_R4833", "R4834_R4834", "R4835_R4835", "R4836_R4836", "R4837_R4837", "R4838_R4838", "R4839_R4839", "R4840_R4840", "R4841_R4841", "R4842_R4842", "R4843_R4843", "R4844_R4844", "R4845_R4845", "R4846_R4846", "R4847_R4847", "R4848_R4848", "R4849_R4849", "R4850_R4850", "R4851_R4851", "R4852_R4852", "R4853_R4853", "R4854_R4854", "R4855_R4855", "R4856_R4856", "R4857_R4857", "R4858_R4858", "R4859_R4859", "R4860_R4860", "R4861_R4861", "R4862_R4862", "R4863_R4863", "R4864_R4864", "R4865_R4865", "R4866_R4866", "R4867_R4867", "R4868_R4868", "R4869_R4869", "R4870_R4870", "R4871_R4871", "R4872_R4872", "R4873_R4873", "R4874_R4874", "R4875_R4875", "R4876_R4876", "R4877_R4877", "R4878_R4878", "R4879_R4879", "R4880_R4880", "R4881_R4881", "R4882_R4882", "R4883_R4883", "R4884_R4884", "R4885_R4885", "R4886_R4886", "R4887_R4887", "R4888_R4888", "R4889_R4889", "R4890_R4890", "R4891_R4891", "R4892_R4892", "R4893_R4893", "R4894_R4894", "R4895_R4895", "R4896_R4896", "R4897_R4897", "R4898_R4898", "R4899_R4899", "R4900_R4900", "R4901_R4901", "R4902_R4902", "R4903_R4903", "R4904_R4904", "R4905_R4905", "R4906_R4906", "R4907_R4907", "R4908_R4908", "R4909_R4909", "R4910_R4910", "R4911_R4911", "R4912_R4912", "R4913_R4913", "R4914_R4914", "R4915_R4915", "R4916_R4916", "R4917_R4917", "R4918_R4918", "R4919_R4919", "R4920_R4920", "R4921_R4921", "R4922_R4922", "R4923_R4923", "R4924_R4924", "R4925_R4925", "R4926_R4926", "R4927_R4927", "R4928_R4928", "R4929_R4929", "R4930_R4930", "R4931_R4931", "R4932_R4932", "R4933_R4933", "R4934_R4934", "R4935_R4935", "R4936_R4936", "R4937_R4937", "R4938_R4938", "R4939_R4939", "R4940_R4940", "R4941_R4941", "R4942_R4942", "R4943_R4943", "R4944_R4944", "R4945_R4945", "R4946_R4946", "R4947_R4947", "R4948_R4948", "R4949_R4949", "R4950_R4950", "R4951_R4951", "R4952_R4952", "R4953_R4953", "R4954_R4954", "R4955_R4955", "R4956_R4956", "R4957_R4957", "R4958_R4958", "R4959_R4959", "R4960_R4960", "R4961_R4961", "R4962_R4962", "R4964_R4964", "R4965_R4965", "R4966_R4966", "R4967_R4967", "R4968_R4968", "R4969_R4969", "R4970_R4970", "R4971_R4971", "R4972_R4972", "R4973_R4973", "R4974_R4974", "R4975_R4975", "R4976_R4976", "R4977_R4977", "R4978_R4978", "R4979_R4979", "R4980_R4980", "R4981_R4981", "R4982_R4982", "R4983_R4983", "R4984_R4984", "R4985_R4985", "R4986_R4986", "R4987_R4987", "R4988_R4988", "R4989_R4989", "R4990_R4990", "R4991_R4991", "R4992_R4992", "R4993_R4993", "R4994_R4994", "R4995_R4995", "R4996_R4996", "R4997_R4997", "R4998_R4998", "R4999_R4999", "R5000_R5000", "R5001_R5001", "R5002_R5002", "R5003_R5003", "R5004_R5004", "R5005_R5005", "R5006_R5006", "R5007_R5007", "R5008_R5008", "R5009_R5009", "R5010_R5010", "R5011_R5011", "R5012_R5012", "R5013_R5013", "R5014_R5014", "R5015_R5015", "R5016_R5016", "R5017_R5017", "R5018_R5018", "R5019_R5019", "R5020_R5020", "R5021_R5021", "R5022_R5022", "R5023_R5023", "R5024_R5024", "R5025_R5025", "R5026_R5026", "R5027_R5027", "R5028_R5028", "R5029_R5029", "R5030_R5030", "R5031_R5031", "R5032_R5032", "R5033_R5033", "R5034_R5034", "R5035_R5035", "R5036_R5036", "R5037_R5037", "R5038_R5038", "R5039_R5039", "R5040_R5040", "R5041_R5041", "R5042_R5042", "R5043_R5043", "R5044_R5044", "R5045_R5045", "R5046_R5046", "R5047_R5047", "R5048_R5048", "R5049_R5049", "R5050_R5050", "R5051_R5051", "R5052_R5052", "R5053_R5053", "R5054_R5054", "R5055_R5055", "R5056_R5056", "R5057_R5057", "R5058_R5058", "R5059_R5059", "R5060_R5060", "R5061_R5061", "R5062_R5062", "R5063_R5063", "R5064_R5064", "R5065_R5065", "R5066_R5066", "R5067_R5067", "R5068_R5068", "R5069_R5069", "R5070_R5070", "R5071_R5071", "R5072_R5072", "R5073_R5073", "R5074_R5074", "R5075_R5075", "R5076_R5076", "R5077_R5077", "R5078_R5078", "R5079_R5079", "R5080_R5080", "R5081_R5081", "R5082_R5082", "R5083_R5083", "R5084_R5084", 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