Nicholas-NVS's repositories
FlavonoidFriday
Flavonoids are specialized metabolites in plants that have numerous functions including protection against abiotic stresses, pigmentation, and repelling herbivores.This repository provides additional background to the #FlavonoidFriday tweets
Bioinformatics-scripts
Repository for Bioinformatics scripts and basic programs developed by L.M.C
Bioinformatica
Pipelines e scripts para análise de Bioinformática
rnaseq_tutorial
Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.
FIELDimageR
FIELDimageR: A R package to analyze orthomosaic images from agricultural field trials. This package is a compilation of functions to analyze pos-mosaicking images from research fields, and allows to: crop the image; remove soil effect; build vegetation indices; rotate the image; build the plot shapefile; extract information for each plot; and evaluate stand count, canopy percentage, and plant height.
GAAS
Genome Assembly and Annotation Service code
PiRATE
PiRATE (Pipeline to Retrieve and Annotate Transposable Elements)
davinciCode
Collection of all scripts and try-out scripts
perlscripts
some small perl scripts
OrthoFinder
Accurate inference of orthologous gene groups made easy. "OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthologous gene group inference accuracy"
gtf_fixer_to_gffread
Script to replace end positions of a GTF file with the sequence size of a single line FASTA file.
perlscripts_jit
All the misc. perl scripts
jcvi
Python utility libraries on genome assembly, annotation and comparative genomics
bio-pipeline
My collection of light bioinformatics analysis pipelines for specific tasks
scripts
General scripts used in the lab. Almost all of them are in core perl, i.e require no modules that don't already come with a perl installation. These script are currently in use by the Lab, so expect full support. This material is based upon work supported by the National Science Foundation under Grant Number EAR-1035955. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.
hyphy
HyPhy: Hypothesis testing using Phylogenies
lskScripts
A placeholder for all my random scripts. Some scripts might eventually graduate and go to their own projects, so don't be surprised if anything leaves in the future.
GWDSR
Wrapper scripts for an integrative analysis workflow for genome-wide detection of selection and recombination
quota-alignment
Guided synteny alignment between duplicated genomes (within specified quota constraint)
kentUtils
UCSC command line bioinformatic utilities
lactad-bioinfo-2013
Exercícios de Perl em Bioinformática - Curso de Bioinformática LaCTAD Unicamp 2013