douglasgscofield

Research bioinformatician

Uppsala UniversityUppsala, Sweden

Pinned Repositories

bioinfo
Various bioinformatics tools
Language:Perl19 5 125
dispersalDiversity
Analyse individual and genetic diversity of dispersal processes in biological populations
Language:R1 1 00
dispr
Degenerate In-Silico PcR
Language:Perl3 1 32
fastrank
R package providing fast ranking for integer and numeric vectors, an alternative to calling .Internal(rank(...))
Language:C3 2 01
hcluster
My git clone of Heng Li's hcluster from http://sourceforge.net/p/treesoft/code/HEAD/tree/branches/lh3/
Language:C++8 1 08
HPF
Convert HPF data from QuickDAQ monitoring machine to TXT or CSV, because files that are too large cannot be converted with the software provided with the machine.
Language:C++0 1 00
PacBio-utilities
Collection of utilities for working with PacBio-based assemblies
Language:Perl13 5 36
readGenalex
R package for reading GenAlEx-format genotype files
Language:R41
sparseMEM-big
Big-genome modification to sparseMEM from Khan et al.
Language:C++3 2 05
tinyutils
Collection of tiny utilities for working on data streams
Language:Awk13 4 15

douglasgscofield's Repositories

douglasgscofield/bioinfo
Various bioinformatics tools
Language:Perl19 5 125
douglasgscofield/PacBio-utilities
Collection of utilities for working with PacBio-based assemblies
Language:Perl13 5 36
douglasgscofield/tinyutils
Collection of tiny utilities for working on data streams
Language:Awk13 4 15
douglasgscofield/hcluster
My git clone of Heng Li's hcluster from http://sourceforge.net/p/treesoft/code/HEAD/tree/branches/lh3/
Language:C++8 1 08
douglasgscofield/dispr
Degenerate In-Silico PcR
Language:Perl3 1 32
douglasgscofield/yoruba
Query and modify BAM file contents; provides functions missing from some other tools
Language:C++2 2 01
douglasgscofield/add-to-Qiime-DB
Small set of scripts to ease the expansion of a Qiime reference database
Language:Perl1 2 01
douglasgscofield/dispersalDiversity
Analyse individual and genetic diversity of dispersal processes in biological populations
Language:R1 1 00
douglasgscofield/MLGtest
Implements a conservative test for asexuality based on the number of observed multilocus genotypes
Language:R1 1 0
douglasgscofield/seqtools-4.28
My version of https://www.sanger.ac.uk/resources/software/seqtools/ 4.28, adds extra dotplot options
Language:C1 1 0
douglasgscofield/HPF
Convert HPF data from QuickDAQ monitoring machine to TXT or CSV, because files that are too large cannot be converted with the software provided with the machine.
Language:C++0 1 00
douglasgscofield/BPCells
Scaling Single Cell Analysis to Millions of Cells
Language:C++0 0
douglasgscofield/branchrates
Calculates branch-specific evolutionary rates for homologous characters
Language:C++
douglasgscofield/chrom-gc
Models chromosome structure to study recombination
Language:C++1 0
douglasgscofield/compleasm
A genome completeness evaluation tool based on miniprot
Language:Python0 0
douglasgscofield/EBC-Perl-Hacks
Repository for the Perl Hacks meeting group in the Evolutionary Biology Centre at Uppsala University
Language:Perl1 01
douglasgscofield/gameteUtils
Set of tools for analysing the genetics and genomics of gametes
Language:Perl
douglasgscofield/GeneticSimLib
Update of John Conery's Genetic Simulation Library
Language:C++1 0
douglasgscofield/K
K implements Kondrashov's 1985 model for genomic mutation, with some extras
Language:C++1 0
douglasgscofield/pathPhynder
A workflow for integrating ancient lineages into present-day phylogenies.
Language:R0 0
douglasgscofield/popgen
Tools for population genetics analysis.
Language:R1 0
douglasgscofield/projecteuler
Solutions in R for problems from https://projecteuler.net/
Language:R1 0
douglasgscofield/psari
Pseudogene discovery
Language:Perl2 01
douglasgscofield/pubs
Repository for scripts, etc. associated with publications
Language:R2 0
douglasgscofield/riker
Reasonable replacements for Picard tools
Language:Shell
douglasgscofield/samla
Examine collection of parallel VCF files and produce consensus variant calls
Language:C++1 0
douglasgscofield/smorgas
Eat samtools' mpileup and do interesting things; for de novo sequencing projects
Language:C++1 0
douglasgscofield/stacksTemplates
Produce SNP-assay templates from Stacks batch files
Language:Perl1 0
douglasgscofield/uppmax
Uppmax-themed repository
Language:Perl1 03
douglasgscofield/whyp
Maximum-likelihood assignment of parentage
Language:R1 02