rsiani

Roberto Siani's starred repositories

interpret

Fit interpretable models. Explain blackbox machine learning.

Language:C++MIT6157 144 438

ggraph

Grammar of Graph Graphics

Language:RNOASSERTION1062 45 329

ggfortify

Define fortify and autoplot functions to allow ggplot2 to handle some popular R packages.

Language:RNOASSERTION527 23 91

parameters

:bar_chart: Computation and processing of models' parameters

Language:RGPL-3.0419 13 572

statsExpressions

Tidy data frames and expressions with statistical summaries 📜

Language:RNOASSERTION311 8 106

graphlayouts

new layout algorithms for network visualizations in R

Language:RNOASSERTION269 9 72

hyphy

HyPhy: Hypothesis testing using Phylogenies

Language:HyPhyNOASSERTION201 22 1319

randomForestSRC

DOCUMENTATION:

Language:CGPL-3.0114 10 165

tidyclust

A tidy unified interface to clustering models

Language:RNOASSERTION107 6 105

ggplate

Create Layout Plots of Biological Culture Plates and Microplates

Language:RNOASSERTION89 4 14

gonomics

A collection of genomics software tools written in Go (golang).

Language:GoBSD-3-Clause77 5 47

fasten

:construction_worker: Fasten toolkit, for streaming operations on fastq files

Language:RustMIT76 5 16

ggokabeito

Colorblind-friendly, qualitative Okabe-Ito Scales for ggplot2 and ggraph

Language:RNOASSERTION46 2 2

packagefinder

Comfortable search for R packages on CRAN, either directly from the R console or with an R Studio add-in

Language:RGPL-3.043 8 8

SuperCRUNCH

A bioinformatics package for creating, filtering, and manipulating supermatrices and phylogenetic datasets using GenBank and/or local sequence data.

Language:PythonGPL-3.041 3 11

hyphy-analyses

HyPhy standalone analyses

Language:PostScriptMIT36 7 47

funkyheatmap

Visualising data frames as funky heatmaps 📊

Language:RNOASSERTION24 2 5

BIRDMAn

Bayesian Inferential Regression for Differential Microbiome Analysis

Language:PythonBSD-3-Clause22 5 46

MD2

MicrobeDirectory 2.0

Language:Jupyter Notebook20 4 17

insect

Informatic Sequence Classification Trees

Language:R14 4 6

MGnifyR

R package for searching, downloading and analysis of EBI MGnify metagenomics data

Language:R12 4 8

ggpcp

Webpage for ggpcp: https://heike.github.io/ggpcp/

Language:RGPL-3.01200

macrosyntR

R package for comparison of synteny conservation at the genome-wide scale.

Language:RGPL-3.012 1 3

nett

"nett" package for community detection in R

Language:RNOASSERTION8 10

bacterialEvolutionMetrics

Scripts in support of publication

Language:Jupyter Notebook7 2 1

OweniaGenome

Annelid functional genomics reveal the origins of bilaterian life cycles - Supplementary Data

Language:Jupyter Notebook600

timesaveR

R package to quickly perform data analysis and reporting tasks that might otherwise be time intensive

Language:RGPL-3.04 2 10

SVVS

Language:PythonMIT300

NetCom2

Language:PythonMIT100

ggCaller

Bifrost graph gene caller.

Language:C++MIT100