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flexdotplot

R package for Flexible dot plots

fusca

Framework for Unified Single-Cell Analysis (FUSCA) is a software package for single-cell data analysis developed in R. At the moment, it contains two modules: 1) CellRouter, for reconstruction of complex single-cell trajectories, and 2) CellComm, to infer intercellular communication networks from scRNA-seq data.

gatk

Official code repository for GATK versions 4 and up

genometornadoplot

genomicsupersignature

Interpretation of RNAseq experiments through robust, efficient comparison to public databases

geocancerprognosticdatasetsretriever

GEO Cancer Prognostic Datasets Retriever is a bioinformatics tool for cancer prognostic dataset retrieval from the GEO website.

gficf

An R implementation of the Gene Frequency - Inverse Cell Frequency method for single cell data normalization

ggdensity

An R package for interpretable visualizations of bivariate density estimates

gget

gget enables efficient querying of genomic databases, such as Ensembl, UniProt, NCBI, directly into a Python or terminal programming environment. It was designed to support genomic data analysis.

ggplot2

An implementation of the Grammar of Graphics in R

ggseg

Plotting tool for brain atlases, in ggplot

glassx

GLASS consortium

gseapy

Gene Set Enrichment Analysis in Python

gwa_tutorial

A comprehensive tutorial about GWAS and PRS

handcalcs

Python library for converting Python calculations into rendered latex.

hands-on-data-analysis-with-pandas-2nd-edition

Materials for following along with Hands-On Data Analysis with Pandas – Second Edition

hippo

Heterogeneity Induced Pre-Processing tOol

ibrap

single-cell RNA-sequencing integrative, benchmarking tool.

immunarch

🧬 Immunarch by ImmunoMind: R Package for Fast and Painless Exploration of Single-cell and Bulk T-cell/Antibody Immune Repertoires

immunedeconv

A unified interface to immune deconvolution methods (CIBERSORT, EPIC, quanTIseq, TIMER, xCell, MCPcounter)

immunesubtypeclassifier

An R package for classification of immune subtypes, in cancer, using gene expression data.

imvigor210corebiologies

http://research-pub.gene.com/IMvigor210CoreBiologies/

in-depth-ngs-data-analysis-course

integration2019

iobr

IOBR is an R package to perform comprehensive analysis of tumor microenvironment and signatures for immuno-oncology.

ktplots

Some tools for plotting single-cell data

leiden

Implementation of the Leiden algorithm called by reticulate in R. (CRAN)

leidenalg

Implementation of the Leiden algorithm for various quality functions to be used with igraph in Python.

liger

R package for integrating and analyzing multiple single-cell datasets

loompy

Python implementation of the Loom file format - http://loompy.org