douglasgscofield/PacBio-utilities

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douglasgscofield/PacBio-utilities

douglasgscofield

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Collection of utilities for working with PacBio-based assemblies

bioinfo

Various bioinformatics tools

tinyutils

Collection of tiny utilities for working on data streams

hcluster

My git clone of Heng Li's hcluster from http://sourceforge.net/p/treesoft/code/HEAD/tree/branches/lh3/

readGenalex

R package for reading GenAlEx-format genotype files

dispr

Degenerate In-Silico PcR

sparseMEM-big

Big-genome modification to sparseMEM from Khan et al.

fastrank

R package providing fast ranking for integer and numeric vectors, an alternative to calling .Internal(rank(...))

snpEffect

Determine the effect of individual SNPs and indels

nestedRanksTest

R package providing a mixed-model Mann-Whitney-Wilcoxon test with nested ranks

yoruba

Query and modify BAM file contents; provides functions missing from some other tools

dispersalDiversity

Analyse individual and genetic diversity of dispersal processes in biological populations

add-to-Qiime-DB

Small set of scripts to ease the expansion of a Qiime reference database

R-package-utilities

Collection of files, templates, tips, etc. to ease the creation and maintenance of R packages

seqtools-4.28

My version of https://www.sanger.ac.uk/resources/software/seqtools/ 4.28, adds extra dotplot options

MLGtest

Implements a conservative test for asexuality based on the number of observed multilocus genotypes

jmers

Kmer-guided processing of jumping reads