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