Joseph F. Ryan (josephryan)

josephryan

Geek Repo

Company:Whitney Laboratory for Marine Bioscience

Location:St. Augustine, Florida, USA

Home Page:http://ryanlab.whitney.ufl.edu

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Joseph F. Ryan's repositories

estimate_genome_size.pl

Scripts to estimate genome size and coverage from kmer distribution generated by jellyfish

alien_index

identify potential non-animal transcripts in animal transcriptomes

Language:PerlLicense:GPL-2.0Stargazers:11Issues:2Issues:3

sowhat

Program to run the SOWH test (likelihood-based test used to compare tree topologies which are not specified a priori)

Language:PerlLicense:GPL-3.0Stargazers:10Issues:7Issues:34

FastqSifter

Separate contaminating reads from FASTQ files (e.g., mitochondria, symbionts, bacterial or human contaminants)

Language:PerlLicense:GPL-3.0Stargazers:9Issues:2Issues:2

Hernandez_Ryan_2021_Recoding

Simulation study of recoding effectiveness

Language:PerlLicense:GPL-3.0Stargazers:7Issues:2Issues:1

matemaker

make artificial mate pairs from long sequences for scaffolding

Language:PerlLicense:GPL-3.0Stargazers:3Issues:2Issues:1

hmm2aln.pl

script to automate gene family phylogeny based using HMM

Language:PerlLicense:GPL-3.0Stargazers:2Issues:2Issues:0

SeaCucumberPhylogenomics

Sea cucumber phylogenomics

Language:PerlLicense:GPL-3.0Stargazers:2Issues:2Issues:0

ctenophore_innexins

Analyses of the innexins of ctenophores

Language:RoffLicense:GPL-3.0Stargazers:1Issues:1Issues:0
Language:PerlLicense:GPL-3.0Stargazers:1Issues:2Issues:0

RyanLabShortReadAssembly

Our pipeline for assembling short reads

Language:PerlLicense:GPL-3.0Stargazers:1Issues:2Issues:0

SELECTINGS

A pipeline to detect positive Darwinian selection in large datasets

Language:PerlLicense:GPL-3.0Stargazers:1Issues:1Issues:0

Steinworth_CnidarianHox

Cnidarian Hox Phylotocol and scripts

Language:PerlLicense:GPL-3.0Stargazers:1Issues:2Issues:0

tmppolar

temporary staging area for polar workshop update

Language:PerlLicense:GPL-3.0Stargazers:1Issues:2Issues:0
License:GPL-3.0Stargazers:0Issues:2Issues:0

RyanLab

Repository for supplementary materials produced by the Ryan Lab

Language:PerlLicense:GPL-2.0Stargazers:0Issues:3Issues:0

2019-Babonis_et_al_trypsins

Files corresponding with Trypsin study by Babonis et al.

Language:PerlLicense:GPL-3.0Stargazers:0Issues:2Issues:0
Language:PerlLicense:GPL-3.0Stargazers:0Issues:2Issues:0
Language:PerlLicense:GPL-3.0Stargazers:0Issues:1Issues:0

bioconda-recipes

Conda recipes for the bioconda channel.

Language:ShellLicense:MITStargazers:0Issues:0Issues:0

Bryozoa_innexin

phylogenetic analysis of lophotrochozoa innexins with a focus on the evolution of bryzoan innexins

License:GPL-3.0Stargazers:0Issues:2Issues:0

Cnidaria_shaker_channels

phylogenetic analyses of shaker K+ channels from Cnidaria

License:GPL-3.0Stargazers:0Issues:2Issues:0

DendroPerl

Port of DendroPy to Perl

Language:PerlStargazers:0Issues:1Issues:0
License:GPL-3.0Stargazers:0Issues:1Issues:0

JFR-PerlModules

Perl extensions for dealing with molecular sequence data formats (FASTA, FASTQ, GFF3, and more)

Language:PerlLicense:GPL-3.0Stargazers:0Issues:2Issues:0

Leys_et_al_Ephydatia_cell_atlas

Analyses from Leys et al. - An atlas of morphology of the freshwater sponge Ephydatia muelleri

Language:RLicense:GPL-3.0Stargazers:0Issues:1Issues:0

Nematostella_DKK

Analysis of DKK genes in Nematostella vectensis

License:GPL-3.0Stargazers:0Issues:2Issues:0

no_transcript_left_behind

use transcriptome to build haplotig-merged assembly

Language:PerlLicense:GPL-3.0Stargazers:0Issues:2Issues:0
License:GPL-3.0Stargazers:0Issues:2Issues:0

SpezHox

Analyses of the Hox genes of the Sea Urchin Echinometra sp. EZ

License:GPL-3.0Stargazers:0Issues:2Issues:0