Pinned Repositories
bio-pipeline
My collection of light bioinformatics analysis pipelines for specific tasks
Bioinformatica
Pipelines e scripts para análise de Bioinformática
Bioinformatics-scripts
Repository for Bioinformatics scripts and basic programs developed by L.M.C
davinciCode
Collection of all scripts and try-out scripts
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.
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
GAAS
Genome Assembly and Annotation Service code
Genome_Skimming_Utilities
gtf_fixer_to_gffread
Script to replace end positions of a GTF file with the sequence size of a single line FASTA file.
Nicholas-NVS's Repositories
Nicholas-NVS/bio-pipeline
My collection of light bioinformatics analysis pipelines for specific tasks
Nicholas-NVS/Bioinformatica
Pipelines e scripts para análise de Bioinformática
Nicholas-NVS/Bioinformatics-scripts
Repository for Bioinformatics scripts and basic programs developed by L.M.C
Nicholas-NVS/davinciCode
Collection of all scripts and try-out scripts
Nicholas-NVS/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.
Nicholas-NVS/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
Nicholas-NVS/GAAS
Genome Assembly and Annotation Service code
Nicholas-NVS/Genome_Skimming_Utilities
Nicholas-NVS/gtf_fixer_to_gffread
Script to replace end positions of a GTF file with the sequence size of a single line FASTA file.
Nicholas-NVS/GWDSR
Wrapper scripts for an integrative analysis workflow for genome-wide detection of selection and recombination
Nicholas-NVS/hyphy
HyPhy: Hypothesis testing using Phylogenies
Nicholas-NVS/jcvi
Python utility libraries on genome assembly, annotation and comparative genomics
Nicholas-NVS/kentUtils
UCSC command line bioinformatic utilities
Nicholas-NVS/lactad-bioinfo-2013
Exercícios de Perl em Bioinformática - Curso de Bioinformática LaCTAD Unicamp 2013
Nicholas-NVS/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.
Nicholas-NVS/manuscripts
Nicholas-NVS/OrthoFinder
Accurate inference of orthologous gene groups made easy. "OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthologous gene group inference accuracy"
Nicholas-NVS/perlscripts
some small perl scripts
Nicholas-NVS/perlscripts_jit
All the misc. perl scripts
Nicholas-NVS/PiRATE
PiRATE (Pipeline to Retrieve and Annotate Transposable Elements)
Nicholas-NVS/quota-alignment
Guided synteny alignment between duplicated genomes (within specified quota constraint)
Nicholas-NVS/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.
Nicholas-NVS/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.
Nicholas-NVS/VcfHunter