Abiud

sanbomics_scripts

scripts and notebooks from sanbomics

pygwalker

PyGWalker: Turn your pandas dataframe into an interactive UI for visual analysis

void

vapour

Typed superset of R

bioinfo-combio

The rendered book can be found at https://liulab-dfci.github.io/bioinfo-combio/

worcs

Rstudio project template and convenience functions for the Workflow for Open Reproducible Code in Science (WORCS)

SeuratExtend

GWalkR

Turn your data frame into a tableau style drag and drop UI interface to build visualization in R.

Huang-Thresholding

A nice thresholding algorithm for bacterial colony isolation

GeneSetCluster2.0

GeneSetCluster 2.0: a comprehensive toolset for summarizing and integrating gene-sets analysis

scTriangulate

scTriangulate is a Python package to mix-and-match conflicting clustering results in single cell analysis and generate reconciled clustering solutions

omnideconv

Unified access to several second-generation deconvolution methods

ggpubr

'ggplot2' Based Publication Ready Plots

scCODA

A Bayesian model for compositional single-cell data analysis

sccomp

Testing differences in cell type proportions from single-cell data.

ggnewscale

Multiple Fill, Color and Other Scales in `ggplot2`

positron

Positron, a next-generation data science IDE

STEM

A Method for Mapping Single-cell and Spatial Transcriptomics Data with Transfer Learning

causal_inference_r_workshop

Causal Inference in R Workshop

UCE

UCE is a zero-shot foundation model for single-cell gene expression data

FriendsDontLetFriends

Friends don't let friends make certain types of data visualization - What are they and why are they bad.

scFoundation

litedown

A lightweight version of R Markdown

drug2cell

Gene group activity utility functions for Scanpy

cellhint

A tool for semi-automatic cell type harmonization and integration

clusterProfiler

:bar_chart: A universal enrichment tool for interpreting omics data

pyLemur

A Python implementation of the LEMUR algorithm for analyzing multi-condition single-cell RNA-seq data.

quarto-webr

Community developed Quarto Extension to Embed webR for HTML Documents, RevealJS, Websites, Blogs, and Books.

scDEED

Single-cell dubious embedding detector (scDED): a statistical method for detecting dubious non-linear embeddings

bioinformatics

:microscope: Path to a free self-taught education in Bioinformatics!