GitPlanet

Cheap and reliable Node.js hosting starts at $3/month, and $1/month static HTML hosting

Created with love in Canada, visit hostnodejs.com today

Feel like to post an Ad? Learn Details
All Projects → arendsee → phylostratr

arendsee / phylostratr

Licence: GPL-3.0 license
An R framework for phylostratigraphy

Programming Languages

r
7636 projects

Labels

bioinformaticsgenomicsgene-annotationphylostratigraphy

Projects that are alternatives of or similar to phylostratr

GCModeller
GCModeller: genomics CAD(Computer Assistant Design) Modeller system in .NET language
Stars: ✭ 25 (+0%)
Mutual labels:  genomics
TADLib
A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains
Stars: ✭ 23 (-8%)
Mutual labels:  genomics
HumanIdiogramLibrary
Resource of human chromosome schematics & images
Stars: ✭ 76 (+204%)
Mutual labels:  genomics
mustache
Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation
Stars: ✭ 38 (+52%)
Mutual labels:  genomics
fq
Command line utility for manipulating Illumina-generated FastQ files.
Stars: ✭ 31 (+24%)
Mutual labels:  genomics
tidygenomics
Tidy Verbs for Dealing with Genomic Data Frames https://const-ae.github.io/tidygenomics/
Stars: ✭ 97 (+288%)
Mutual labels:  genomics
phastaf
Identify phage regions in bacterial genomes for masking purposes
Stars: ✭ 22 (-12%)
Mutual labels:  genomics
adapt
A package for designing activity-informed nucleic acid diagnostics for viruses.
Stars: ✭ 16 (-36%)
Mutual labels:  genomics
BALSAMIC
Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer
Stars: ✭ 29 (+16%)
Mutual labels:  genomics
indelope
find large indels (in the blind spot between GATK/freebayes and SV callers)
Stars: ✭ 38 (+52%)
Mutual labels:  genomics
mlst check
Multilocus sequence typing by blast using the schemes from PubMLST
Stars: ✭ 22 (-12%)
Mutual labels:  genomics
graphsim
R package: Simulate Expression data from igraph network using mvtnorm (CRAN; JOSS)
Stars: ✭ 16 (-36%)
Mutual labels:  genomics
region-plot
A tool to plot significant regions of GWAS
Stars: ✭ 20 (-20%)
Mutual labels:  genomics
bio-dockers
🐳 Bio-dockers: dockerized bioinformatic tools
Stars: ✭ 33 (+32%)
Mutual labels:  genomics
macrel
Predict AMPs in (meta)genomes and peptides
Stars: ✭ 34 (+36%)
Mutual labels:  genomics
variantkey
Numerical Encoding for Human Genetic Variants
Stars: ✭ 32 (+28%)
Mutual labels:  genomics
dee2
Digital Expression Explorer 2 (DEE2): a repository of uniformly processed RNA-seq data
Stars: ✭ 32 (+28%)
Mutual labels:  genomics
bxtools
Tools for analyzing 10X Genomics data
Stars: ✭ 39 (+56%)
Mutual labels:  genomics
MindTheGap
MindTheGap is a SV caller for short read sequencing data dedicated to insertion variants (all sizes and types). It can also be used as a local assembly tool.
Stars: ✭ 30 (+20%)
Mutual labels:  genomics
gnomix
A fast, scalable, and accurate local ancestry method.
Stars: ✭ 36 (+44%)
Mutual labels:  genomics
View All Similar Projects ➔

unstable Travis-CI Build Status Coverage Status DOI

phylostratr

Predict and explore the age of genes using phylostratigraphic methods.

Phylostratr Workflow

Installation

You can install from GitHub with:

library(devtools)
install_github("arendsee/phylostratr")

Dependencies

  • NCBI BLAST+ - blastp (the protein BLAST command) must be in PATH. You can tell if blastp is properly installed by calling blastp -help from the command line.

Citation

Zebulun Arendsee, Jing Li, Urminder Singh, Arun Seetharam, Karin Dorman,
Eve Syrkin Wurtele (2019) "phylostratr: A framework for phylostratigraphy." Bioinformatics. https://doi.org/10.1093/bioinformatics/btz171

Funding

This work is funded by the National Science Foundation grant:

NSF-IOS 1546858 Orphan Genes: An Untapped Genetic Reservoir of Novel Traits

Note that the project description data, including the texts, logos, images, and/or trademarks, for each open source project belongs to its rightful owner. If you wish to add or remove any projects, please contact us at [email protected].