Single-cell RNA data analysis using R (Seurat) , Python (Scanpy), and Julia.

Bystro genetic analysis (annotation, filtering, statistics)

Bioinformatics containers

RNA sequencing analysis software

An ensemble of functions for easier and quicker preliminary microbiome analyses

An application for DNA sequence analysis written in Scala and deployed using Apache Spark&Hadoop.

is an open-source LIMS (laboratory Information Management System) for Next Generation Sequencing sample management, statistics and reports, and bioinformatics analysis service management.

CoNSEnsX - Complience of NMR-derived Structural Ensembles with Experimental Data

a single copy gene analysis pangenome which allows for the orthology already computed and allows for the alignment and phylogeny building using three alignment approaches and also allows for the GTRCAT and GTRGAMA model with 1000 bootstrap. To check the file conversion it iterates the first files at the start and see if the number matches

a command line utility coded to incorporate all types of the plots for the single cell analysis plus incoporated some new ones. This will be updated regularly.After finishing all of the additions, I will add the shiny visualization also.

plant resistance gene miner which uses a regular expression plus a web scrap approach and given a resistance gene id, it will return the genbank id

slurm and pbs scripts for illumina and long read genome assembly, transcriptome, metagenomics and comparative analysis

this function takes ids file with the gene of interest and the phytozome gff files and will fetch the pacid for the genes of interest.

There is no function to fetch automatically the information on the reported pubmed articles links in the tair to be used for the language models, so i coded this function which will take the tair information, a gene or locus tag and will fetch the corresponding pubmed and then from the pubmed the corresponding abstracts

Find motifs enriched around prominent crosslinks

Bu sayfada Biyoinformatik analizler ile ilgili eğitim materyalleri bulunmaktadır.

CWL based Bioinformatics Workflows

set of helper tools for bu-isciii management of its core services portfolio.

GCP for Bioinformatics Researchers

Code for the manuscript "Identifying Optimal Substrate Classes of Membrane Transporters"