andrewparkermorgan

#! /usr/bin/env python3
"""
interpolate_cM.py
Annotate a VCF file with genetic position of sites by (linear) interpolation on a user-supplied genetic map.
"""

import os
import sys
import time
import argparse

andrewparkermorgan

#! /usr/bin/env python
"""
jobber.py
Summarize status of running jobs under SLURM scheduler.
"""

from __future__ import print_function

import os
import sys

andrewparkermorgan

# rnaseq.R
# plots related to RNAseq data

library(GenomicAlignments)
library(GenomicRanges)
library(ggplot2)
library(grid)
#library(gtable) # for combining plots vertically

#' Make a 'sashimi plot': coverage plus splice events

andrewparkermorgan

#' Draw a haplotype bifurcation diagram
#' 
#' @param hh an object of class `haplohh` (from rehh package)
#' @param focal genomic position of the focal site
#' @param left extend haplotypes this many (variant) sites to the left of the focal site
#' @param right extend haplotypes this many (variant) sites to the right of the focal site
#' @param palette name of an RColorBrewer palette used for colors
#' @param reverse logical; if `TRUE`, put derived allele in upper panel
#' @param relabel a named list to use for re-labelling panels; default labels are 'ancestral' and 'derived'
#' @param ... other arguments passed through to rehh::bifurcation.diagram()