peter.ralph > methods

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1Well-posed, ill-posed, and intermediate problems with applications
Y. Petrov, and V. Sizikov. Walter de Gruyter, (2005)
12 years ago by @peter.ralph
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methods
inverse_problems
ill-posed_problems
review
methodsinverse_problemsill-posed_problemsreview
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1Watterson estimators for Next Generation Sequencing: from trios to autopolyploids
L. Ferretti, and S. Ramos-Onsins. (2013)cite arxiv:1309.4380.
9 years ago by @peter.ralph
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methods
pairwise_divergence
low_coverage
statistics
methodspairwise_divergencelow_coveragestatistics
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1Visualizing spatial population structure with estimated effective migration surfaces
D. Petkova, J. Novembre, and M. Stephens. Nat Genet, 48 (1): 94-100 (January 2016)
8 years ago by @peter.ralph
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methods
resistance_distance
spatial_coalescent
effective_resistance
methodsresistance_distancespatial_coalescenteffective_resistance
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1Visualizing spatial population structure with estimated effective migration surfaces
D. Petkova, J. Novembre, and M. Stephens. bioRxiv, (November 2014)
10 years ago by @peter.ralph
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Voronoi_cells
methods
isolation_by_distance
resistance_distance
population_structure
Voronoi_cellsmethodsisolation_by_distanceresistance_distancepopulation_structure
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1Validation of close-kin mark–recapture (CKMR) methods for estimating population abundance
D. Ruzzante, G. McCracken, B. Førland, J. MacMillan, D. Notte, C. Buhariwalla, J. Mills Flemming, and H. Skaug. Methods in Ecology and Evolution, 10 (9): 1445-1453 (2019)
4 years ago by @peter.ralph
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methods
pedigrees
close-kin-mark-recapture
methodspedigreesclose-kin-mark-recapture
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1Using linkage maps to correct and scaffold de novo genome assemblies: methods, challenges, and computational tools
J. Fierst. Front Genet, (2015)
9 years ago by @peter.ralph
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methods
bioinformatics
review
linkage
assembly
methodsbioinformaticsreviewlinkageassembly
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1Using circuit theory to model connectivity in ecology, evolution, and conservation
B. McRae, B. Dickson, T. Keitt, and V. Shah. Ecology, 89 (10): 2712--2724 (2008)
8 years ago by @peter.ralph
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landscape_genetics
methods
resistance_distance
landscape_geneticsmethodsresistance_distance
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1Unified framework to evaluate panmixia and migration direction among multiple sampling locations
P. Beerli, and M. Palczewski. Genetics, 185 (1): 313-326 (May 2010)
6 years ago by @peter.ralph
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migration_estimation
methods
MCMC
migration_estimationmethodsMCMC
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1Tree-based QTL mapping with expected local genetic relatedness matrices
V. Link, J. Schraiber, C. Fan, B. Dinh, N. Mancuso, C. Chiang, and M. Edge. bioRxiv, (2023)
a year ago by @peter.ralph
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relatedness
treeWAS
methods
tree_sequence
QTL
relatednesstreeWASmethodstree_sequenceQTL
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1The relative power of genome scans to detect local adaptation depends on sampling design and statistical method
K. Lotterhos, and M. Whitlock. Molecular Ecology, 24 (5): 1031--1046 (2015)
7 years ago by @peter.ralph
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scan_for_selection
methods
local_adaptation
F_ST
simulation_study
scan_for_selectionmethodslocal_adaptationF_STsimulation_study
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1The Horseshoe+ Estimator of Ultra-Sparse Signals
A. Bhadra, J. Datta, N. Polson, and B. Willard. (2015)cite arxiv:1502.00560.
8 years ago by @peter.ralph
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Bayesian
methods
sparsification
regularization
statistics
Bayesianmethodssparsificationregularizationstatistics
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2The history of African gene flow into Southern Europeans, Levantines, and Jews
P. Moorjani, N. Patterson, J. Hirschhorn, A. Keinan, L. Hao, G. Atzmon, E. Burns, H. Ostrer, A. Price, and D. Reich. PLoS Genet., (April 2011)
13 years ago by @peter.ralph
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human_genome
SNP
admixture
methods
gene_flow
LD
PCA
human_genomeSNPadmixturemethodsgene_flowLDPCA
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1The genome sequence of the colonial chordate, Botryllus schlosseri
A. Voskoboynik, N. Neff, D. Sahoo, A. Newman, D. Pushkarev, W. Koh, B. Passarelli, H. Fan, G. Mantalas, K. Palmeri and 9 other author(s). Elife, (2013)
10 years ago by @peter.ralph
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genome_sequence
long_reads
methods
sequencing_technology
genome_sequencelong_readsmethodssequencing_technology
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3The control of the false discovery rate in multiple testing under dependency
Y. Benjamini, and D. Yekutieli. The Annals of Statistics, 29 (4): 1165--1188 (August 2001)
5 years ago by @peter.ralph
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methods
false_discovery_rate
statistics
methodsfalse_discovery_ratestatistics
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1Testing for ancient admixture between closely related populations
E. Durand, N. Patterson, D. Reich, and M. Slatkin. Mol Biol Evol, 28 (8): 2239-2252 (August 2011)
9 years ago by @peter.ralph
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ancient_genomes
methods
ABBA-BABA
population_genetics
introgression
ancient_genomesmethodsABBA-BABApopulation_geneticsintrogression
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1Testing environmental and genetic effects in the presence of spatial autocorrelation
F. Rousset, and J. Ferdy. Ecography, (2014)
10 years ago by @peter.ralph
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isolation_by_environment
methods
isolation_by_distance
spatial_statistics
isolation_by_environmentmethodsisolation_by_distancespatial_statistics
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1Strategies for processing and quality control of Illumina genotyping arrays
S. Zhao, W. Jing, D. Samuels, Q. Sheng, Y. Shyr, and Y. Guo. Briefings in Bioinformatics, 19 (5): 765-775 (February 2017)
4 years ago by @peter.ralph
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genotype_arrays
genotyping
methods
statistics
genotype_arraysgenotypingmethodsstatistics
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1Statistical inference for stochastic simulation models – theory and application
F. Hartig, J. Calabrese, B. Reineking, T. Wiegand, and A. Huth. Ecology Letters, 14 (8): 816--827 (2011)
8 years ago by @peter.ralph
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synthetic_likelihood
methods
approximate_bayesian_computation
review
simulation-based_inference
synthetic_likelihoodmethodsapproximate_bayesian_computationreviewsimulation-based_inference
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1Statistical data analysis
G. Cowan. Oxford University Press, USA, (1998)
12 years ago by @peter.ralph
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methods
inverse_problems
review
data_unfolding
physicists
statistics
methodsinverse_problemsreviewdata_unfoldingphysicistsstatistics
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2SPLATCHE2: a spatially explicit simulation framework for complex demography, genetic admixture and recombination
N. Ray, M. Currat, M. Foll, and L. Excoffier. Bioinformatics, 26 (23): 2993-2994 (December 2010)
8 years ago by @peter.ralph
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software
methods
simulation
spatial_structure
coalescent_theory
softwaremethodssimulationspatial_structurecoalescent_theory
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1RPubs - Visual Raster Cheatsheet

1Mapping and GIS’ing in R | Animal Movements

publications (hide)279
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1Well-posed, ill-posed, and intermediate problems with applications

1Watterson estimators for Next Generation Sequencing: from trios to autopolyploids

1Visualizing spatial population structure with estimated effective migration surfaces

1Visualizing spatial population structure with estimated effective migration surfaces

1Validation of close-kin mark–recapture (CKMR) methods for estimating population abundance

1Using linkage maps to correct and scaffold de novo genome assemblies: methods, challenges, and computational tools

1Using circuit theory to model connectivity in ecology, evolution, and conservation

1Unified framework to evaluate panmixia and migration direction among multiple sampling locations

1Tree-based QTL mapping with expected local genetic relatedness matrices

1The relative power of genome scans to detect local adaptation depends on sampling design and statistical method

1The Horseshoe+ Estimator of Ultra-Sparse Signals

2The history of African gene flow into Southern Europeans, Levantines, and Jews

1The genome sequence of the colonial chordate, Botryllus schlosseri

3The control of the false discovery rate in multiple testing under dependency

1Testing for ancient admixture between closely related populations

1Testing environmental and genetic effects in the presence of spatial autocorrelation

1Strategies for processing and quality control of Illumina genotyping arrays

1Statistical inference for stochastic simulation models – theory and application

1Statistical data analysis

2SPLATCHE2: a spatially explicit simulation framework for complex demography, genetic admixture and recombination

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