R code in R Markdown used for ucm genomes and genome analysis course

Multiple sequence alignment tool that builds on the concept of seed-and-extend algorithms

estimation of the genome size for the illumina reads, only for the pre-screening purposes and includes a R function also.

A useful python package for working on genomic coordinates.

This code compares the theoretical and practical length distributions of fragments.

MAGset is a tool to analyze and compare MAGs of known species

A human-first SV annotation snakemake pipeline based on nanotatoR working with optical mapping (Bionano Genomics) data

MRA, A Novel Multi-head Algorithm to Discover all Tandem Repeats in One Scan of DNA Sequences.

Scrapes all the results of all the genome analysis performed by MiGA Online web tool and wirte them in a file.

Create a Bioconductor/R SDK for Arvados

App to identify if a given DNA sequence is present in a viral genome repository. If found, it also gives the location and the protein it was a part of.

Analysis of input alphabet sequential data

Raw data and code for the Genomic Analysis of Singles and Pools (GASP) project - https://doi.org/10.1099/mgen.0.001111

Optimal AlphaMissense threshold based on VKGL variant classifications

Some snippet of code related to bioinformatics

Java Clients for the Regulatory Sequence Analysis Tools (RSAT) REST API

A simple tool to generate hierarchical clustering trees from nucleotide sequences. Supports a number of distance metrics and clustering algorithms. Includes a large testset of SARSCOV2 genomes.

Analysis of drought metagenomic data using ENNB methods

Front-end for views and tables in web interface

A set of functions which will provide easy access and cleaned gff from tair and uses a dataframe and datascience approach to get the systematic tair ids and their coordinates from the tair 10 gff version. It can be applied to any version of the tair for getting the systematic retrival of the tair ids.