Gaurav Sablok's repositories
codingplotter
a coding plotter for the protein annotations coming from the annotation of the genome using the protein hints and to extract and plot the specific length estimates.
nextflow-pacbiohifi
a nextflow pacbiohifi for the genome assembly from the pacbiohifi. It also includes supports for the visualization and genome assessment.
protein-annotator
python package to analyze the protein coding regions for the genome annotation. It uses the miniprot for the alignment and gives you all the protein predicted mRNA, coding regions and other exon positions.
pacbiohifi-analyzer
a pacbiohifi analyzer for the pacbio hifi reads and gives all the information for the pacbiohifi reads from raw to the graph alignments
arabidopsis-maf-cap-accessions
arabidopsis-maf-cap-accessions. genome extraction, alignments, visualization, phylogenomics, ancestral tree
coding-stitcher-pangenome
a coding sticher for genome annotations, which stitch all your coding regions coming out of the exon alignments and will produce the gene visualization for the pangenome
data-driven-web-apps-with-flask
Course demo code and other hand-out materials for our data-driven web apps in Flask course
deeplearning4nlp-tutorial
Hands-on tutorial on deep learning with a special focus on Natural Language Processing (NLP)
evoseq-genome-informatics
a R package for the genomes annotations to phylogeny. a R package for the analysis of the specific genes from the sequenced genomes.
flux-models-ruby
implementation of mathematical models in ruby bindings and also as shards for the crystal. This repository will be updated regularly for the complete integration
genome-annotation-multivisual
dplyr version of visualization of all the coding regions for a specific ids from protein alignment.
genome-annotation-visualizer
a R function part to visualizae the genes coming from the genome alignment proteome annotations. This is a part of the evoseq R package
GenomeAnnotation
Best practices and workflow for genome annotation
genomehifi-contiguity
a conda yaml for the genomehifi-contiguity that will allow you to create the environment for all the analysis.
intergenic-extractor
extracting all the intergenic regions from the genome annotation using the protein alignments.
miniprot-protein-annotator
a protein coding regions annotator that will take the alignment file in the PAF/GFF format and will extract the complete coding regions and prepares them for deep learning.
ML-For-Beginners
12 weeks, 26 lessons, 52 quizzes, classic Machine Learning for all
mRNAplotter
plotting tools for the mRNA from the proteome to the genome anntoation. Produces a tab delimited files with the start and the stop of the mRNAs
ontologies-semanticweb
a ontology to the relation patcher that will prepare the distance implementation. It will prepare the files for the nextworkx also.
ontologyanalyzer
python package for the genome annotations, semantic web and graph implementation on the ontologies.
pacbiohifi-meryl
plotting tools for pacbiohifi meryl hapmers and yak kmers
r-package-backup
r function for the R package installation
ruby-gems-bioinformatics
a collection of the ruby gems that are of the frequent use in my bioinformatics analysis and also for the nominal task.
scala-sbt-class-mapper
a scala sbt class for making the class based mapper for the genome alignment and parsing them for the visual inference
scaling-kmers-neural
from word segmentation to neural kmers
semanticweb-ontologies-prepare
generating the ontology graphs and the system relationship.
smile
Statistical Machine Intelligence & Learning Engine
snp-extract
extracting all the snp sites for the panache and then estimating a identity matrix.
visualfreq
alignment visualization and phylogeny plotting for genome aliged regions.