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Prokka: rapid prokaryotic genome annotation. Prokka is one of the most cited annotation command line tools for microbial genome annotations.

This package primarily identifies variants in mitochondrial genomes from BAM alignment files. It filters these variants to remove RNA editing events then estimates their evolutionary relationship (i.e. their phylogenetic tree) and groups single cells into clones. It also visualizes the mutations and providing additional genomic context.

Find the most characteristic gene ontology terms for groups of human genes. This package was created as a part of the thesis which was developed under the auspices of MI^2 Group (http://mi2.mini.pw.edu.pl/, https://github.com/geneticsMiNIng).

R-based computational framework for a comprehensive in silico analysis of circRNAs. This computational framework allows to combine and analyze circRNAs previously detected by multiple publicly available annotation-based circRNA detection tools. It covers different aspects of circRNAs analysis from differential expression analysis, evolutionary conservation, biogenesis to functional analysis.

Download genome and assembly reports from NCBI

Provides functionalities to translate gene or protein identifiers between state-of-art biological databases: CARD (<https://card.mcmaster.ca/>), NCBI Protein, Nucleotide and Gene (<https://www.ncbi.nlm.nih.gov/>), UniProt (<https://www.uniprot.org/>) and KEGG (<https://www.kegg.jp>). Also offers complementary functionality like NCBI identical proteins or UniProt similar genes clusters retrieval.

This package implements inferential methods to compare gene lists in terms of their biological meaning as expressed in the GO. The compared gene lists are characterized by cross-tabulation frequency tables of enriched GO items. Dissimilarity between gene lists is evaluated using the Sorensen-Dice index. The fundamental guiding principle is that two gene lists are taken as similar if they share a great proportion of common enriched GO items.

Reduce and visualize lists of Gene Ontology terms by identifying redudance based on semantic similarity.