vjmarteau

fzf

:cherry_blossom: A command-line fuzzy finder

overleaf

A web-based collaborative LaTeX editor

obsidian-dataview

A data index and query language over Markdown files, for https://obsidian.md/.

obsidian-kanban

Create markdown-backed Kanban boards in Obsidian.

scvi-tools

Deep probabilistic analysis of single-cell and spatial omics data

scikit-learn-intelex

Intel(R) Extension for Scikit-learn is a seamless way to speed up your Scikit-learn application

shimmering-obsidian

Alfred Workflow with dozens of features for controlling your Obsidian vault.

single-cell-best-practices

https://www.sc-best-practices.org

ffq

A tool to find sequencing data and metadata from public databases.

pymde

Minimum-distortion embedding with PyTorch

patterns

A curated collection of Nextflow implementation patterns

cNMF

Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data

SComatic

A tool for detecting somatic variants in single cell data

decoupler-py

Python package to perform enrichment analysis from omics data.

rapids_singlecell

Rapids_singlecell: A GPU-accelerated tool for scRNA analysis. Offers seamless scverse compatibility for efficient single-cell data processing and analysis.

scDesign3

scDesign3 generates realistic in silico data for multimodal single-cell and spatial omics

luca

Single-cell Lung Cancer Atlas with 1.2M cells

tutorial_DESeq2_contrasts

sparseMatrixStats

Implementation of the matrixStats API for sparse matrices

geofetch

Builds a PEP from SRA or GEO accessions

Mowgli

Single-cell multi-omics integration using Optimal Transport

COSG

Accurate and fast cell marker gene identification with COSG

depmap

Cancer Dependency Map package

nxfvars

Access nextflow variables from python scripts or notebooks

setup-singularity

GitHub action to setup singularity

setup-nextflow

A GitHub action to install Nextflow

nf-deseq2

A RNA-seq differential expression analysis pipeline downstream of nf-core/rnaseq.

glacier_climate_plots

some workflows to plot some figures related to glaciers and climate

alps_future

c13ms

R package for the statistical and functional analysis of 13C labelling data