kfwins2022's Projects
Workshop materials for shotgun metagenomics
:mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes
Adjustment for Confounding Factors using Principal Coordinate Analysis
kmer- and matrix-factorization-based classifier for metagenomics data
Ambiguous Nucleotide Tool (ANT), software for generating and evaluating degenerate codons for natural and expanded genetic codes.
A curated list of awesome R packages, frameworks and software.
Collection of scripts for bacterial genomics
A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences
Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
BEAV: Bacterial Element Annotation reVamped
Bacterial Isolate Genome Sequence Database (BIGSdb): A platform for gene-by-gene bacterial population annotation and analysis.
Find CRISPRS in genomes using pilercr & draws a matrix
Practical Introduction to Bioinformatics and Systems Biology with R (mainly)
A PyTorch Basecaller for Oxford Nanopore Reads
A fast and sensitive gapped read aligner
BRIG is a cross-platform (Windows/Mac/Unix) application that can display circular comparisons between a large number of genomes, with a focus on handling genome assembly data.
A single molecule sequence assembler for genomes large and small.
Inference of homologous recombination in bacteria using whole genome sequences
In this repository, you will find some scripts and commands to perform specific comparative genomics analysis
:exclamation:Ā ThisĀ isĀ aĀ read-onlyĀ mirrorĀ ofĀ theĀ CRANĀ RĀ packageĀ repository. CSESAĀ āĀ CRISPR-BasedĀ SalmonellaĀ EntericaĀ SerotypeĀ Analyzer
Detecting methylation using signal-level features from Nanopore sequencing reads
Pathway prediction methylation
DegenPrimer is a tool to check the quality of degenerate primers by simulating PCR
A program for degenerate primer design for broad taxonomic-range PCR for microbial ecology studies
An R package for a rapid differential gene presence analysis between similar genomes
:dragon: :fly: Assemble bacterial isolate genomes from Nanopore reads
De novo assembler for single molecule sequencing reads using repeat graphs
Genome Assembly and Annotation Pipeline for Bacteria Pacbio
An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences