Sivasankar Palaniappan's repositories
anvio-An-analysis-and-visualization-platform-for-omics-data
An analysis and visualization platform for 'omics data
BacArena
agent based modelling
beav-bacterial-genome-and-mobile-element-annotation-pipeline
BEAV: Bacterial Element Annotation reVamped
cgview_comparison_tool
The CGView Comparison Tool (CCT) is a package for visually comparing bacterial, plasmid, chloroplast, and mitochondrial sequences.
COGclassifier
A tool for classifying prokaryote protein sequences into COG(Cluster of Orthologous Genes) functional category
dorado
Dorado-Oxford Nanopore's Basecaller
EasyMicroPlot
R package for downstream Microbiome analysis
gapseq---Bacterial-gene-pathway-finder
Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks
GeneTonic
Enjoy your transcriptomic data and analysis responsibly - like sipping a cocktail
iModulonsDB_modulome-workflow
Workflow to download, process, and explore microbial RNA-seq data from NCBI SRA
medium-unlimited
A browser extension to read medium.com articles for free without membership.
MGCplotter
Microbial Genome Circular plotting tool for comparative genomics using Circos
MicrobeAnnotator
Pipeline for metabolic annotation of microbial genomes
ORForise
Comparison pipeline for Prokaryote Protein Coding Gene Predictors
Panseq
Pan-genomic sequence analysis
paprica
paprica - PAthway PRediction by phylogenetIC plAcement
PPanGGOLiN
Build a partitioned pangenome graph from microbial genomes
PyComplexHeatmap
PyComplexHeatmap: A Python package to plot complex heatmap (clustermap)
pyGenomeViz
A genome visualization python package for comparative genomics
pymodulon
Python package for analyzing and visualizing iModulons
R-graph-gallery
A website that displays hundreds of R charts with their code
RRNPP_detector
A tool to detect RRNPP-type quorum sensing systems
SCARAP
A toolkit for prokaryotic comparative genomics
scGPT
scGPT: toward building a foundation model for single-cell multi-omics using generative AI
SegAlign
A Scalable GPU-Based Whole Genome Aligner, published in SC20: https://doi.ieeecomputersociety.org/10.1109/SC41405.2020.00043
UpSetR
An R implementation of the UpSet set visualization technique published by Lex, Gehlenborg, et al..
xai_growth
Explainable machine learning models to identify metabolic reactions significantly affecting bacterial growth under different carbon source conditions