Pinned Repositories
203.328
Module 6 Lab Resources – Genome Analysis 203.328
2D_FIR_distribution
Code to calculate 5ʹ and 3ʹ distances to the nearest gene
3D_contact_distribution
Code to calculate 3D contact distributions for subsets of genes
admixture_estimator
adwave
Wavelet analysis of genomic data from admixed populations
filtFst
filtFst calculates Fst, a measure of population differentiation due to genetic structure
frequency_diff
Calculate probability of allele frequency differences by resampling
hybridRNAsim
Simulating 'neutral' gene expression patterns in hybrids and their progenitors
mapcount
Counts read hits against a reference gene set
recomb
The recomb package simulates and summarizes genetic datasets with recombination rates that change over time.
mpcox's Repositories
mpcox/filtFst
filtFst calculates Fst, a measure of population differentiation due to genetic structure
mpcox/frequency_diff
Calculate probability of allele frequency differences by resampling
mpcox/203.328
Module 6 Lab Resources – Genome Analysis 203.328
mpcox/2D_FIR_distribution
Code to calculate 5ʹ and 3ʹ distances to the nearest gene
mpcox/3D_contact_distribution
Code to calculate 3D contact distributions for subsets of genes
mpcox/admixture_estimator
mpcox/adwave
Wavelet analysis of genomic data from admixed populations
mpcox/hybridRNAsim
Simulating 'neutral' gene expression patterns in hybrids and their progenitors
mpcox/mapcount
Counts read hits against a reference gene set
mpcox/recomb
The recomb package simulates and summarizes genetic datasets with recombination rates that change over time.
mpcox/asiamodel
Testing site for msprime coalescent models of Asian demography
mpcox/bali_lattice
Javascript Bali lattice model
mpcox/drifter
Simulate genetic drift and sampling error in population genetic samples
mpcox/fasta_select
Extract specified sequences from a fasta file
mpcox/filter_fasta
Filter fasta sequences by size
mpcox/gene_ordering
Code to simulate random gene loss in the yeast genome
mpcox/gst_prime
Implementation of a standardized genetic differentiation measure
mpcox/hapmatch
Determines lineages with given ingroup and outgroup frequencies in coalescent genealogies
mpcox/IMgc
Finds the largest non-recombining block in a DNA alignment
mpcox/lesson-example
Example lesson using The Carpentries lesson template.
mpcox/microsat
Microsat simulates the evolution of linked and unlinked microsatellites using the coalescent.
mpcox/models
Models for website hosting
mpcox/monte
Statistical significance of high and low mutation rates
mpcox/msrho
Calculates the rho statistic for coalescent genealogies
mpcox/mstree
Calculates TMRCA and the minimum clade proportion for coalescent genealogies
mpcox/seqStats
Calculate sequence statistics of fasta files
mpcox/summarize_contigs
Characterize contigs in a fasta file, including telomere information
mpcox/update
Automate Linux updates