Pinned Repositories
2023-01-31-genomicsdc
bioawk-tutorial
CAFE
Analyze changes in gene family size and provide a statistical foundation for evolutionary inferences.
carpentries-workshop
Corvid_SVpopgen
SV_analysis_for_Dpse_and_Dper
javibio-git's Repositories
javibio-git/SV_analysis_for_Dpse_and_Dper
javibio-git/2023-01-31-genomicsdc
javibio-git/CAFE
Analyze changes in gene family size and provide a statistical foundation for evolutionary inferences.
javibio-git/carpentries-workshop
javibio-git/Corvid_SVpopgen
javibio-git/course20
Deep Learning for Coders, 2020, the website
javibio-git/deeplearning-biology
A list of deep learning implementations in biology
javibio-git/EDTA
Extensive de-novo TE Annotator
javibio-git/FEELnc
FEELnc : FlExible Extraction of LncRNA
javibio-git/javibio-git.github.io
javibio-git/merqury
k-mer based assembly evaluation
javibio-git/minimap2
A versatile pairwise aligner for genomic and spliced nucleotide sequences
javibio-git/mutation_unphased
javibio-git/np_tut_breastcancer
Numpy and matplotlib tutorial for beginners using a breastcancer dataset
javibio-git/OrthNet
CLfinder-OrthNet, a pipeline to encode orthologs from multiple genomes and their evolutionary history into networks (OrthNets) based on co-linearity between them. OrthNets enable detection of all orthologous gene groups that share the same evolutionary history, using a search based on network topology
javibio-git/Parsing-RepeatMasker-Outputs
Few scripts facilitating the extraction of info from Repeat Masker .out files
javibio-git/pbipa
Improved Phased Assembler
javibio-git/Pegoscapus_Annotation_Project
This repository details the protocol used to conduct a comprehensive genome annotation using Maker.
javibio-git/pilon
Pilon is an automated genome assembly improvement and variant detection tool
javibio-git/RepEnrich2
RepEnrich2 is an updated method to estimate repetitive element enrichment using high-throughput sequencing data.
javibio-git/rescan
A command line tool for inferring the locations of repeat expansions and other structural variation from paired-end short read sequencing data
javibio-git/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.
javibio-git/SalmonTE
SalmonTE is an ultra-Fast and Scalable Quantification Pipeline of Transpose Element (TE) Abundances
javibio-git/TEanalysis
Analysis of TE contribution to features (transcripts or simple features). Includes utils to test enrichment.
javibio-git/TElocal
A package for quantifying transposable elements at a locus level for RNAseq datasets.
javibio-git/TEtranscripts
A package for including transposable elements in differential enrichment analysis of sequencing datasets.
javibio-git/toyExample
What the Package Does (One Line, Title Case)
javibio-git/tutorials
Tutorials on phylogenetic and phylogenomic inference
javibio-git/twisst
Topology weighting by iterative sampling of sub-trees
javibio-git/workshop-popgenome
Tutorial about R package PopGenome