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siglasso

Optimizing Cancer Mutation Signatures Jointly with Sampling Likelihood

signac

An analytics package for single cell data

sigprofilerextractor

SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.

single-cell-metabolic-landscape

Pipeline for characterizing metebolic heterogeneity from single-cell RNA-seq data

single-cell-tutorial

Single cell current best practices tutorial case study for the paper:Luecken and Theis, "Current best practices in single-cell RNA-seq analysis: a tutorial"

single-nuclei-epigenomic-and-transcriptomic-landscape-in-alzheimer-disease

Single-nuclei RNA-seq and ATAC-seq in Alzheimer's disease

singler

SingleR: Single-cell RNA-seq cell types Recognition (legacy version)

sky

skylab

Soon to be deprecated in favor of broadinstitute/warp github repo. Previously: Secondary analysis pipelines

soupx

R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data

spotlight

Spatial Transcriptomics Capture Location Deconvolution

swne

Similarity Weighted Nonnegative Embedding (SWNE), a method for visualizing high dimensional datasets

ted

a fully Bayesian approach to deconvolve tumor microenvironment

tidyverse

Easily install and load packages from the tidyverse

tiedie

Tied Diffusion for Subnetwork Discovery (TieDIE)

tldr-python-client

Python command-line client for tldr pages

tnbc_analysis

Code to reproduce TNBC analysis and figures

topometry

A comprehensive dimensional reduction framework to recover the latent topology of high-dimensional data.

transformergo

tweedieverse

Differential analysis of multi-omics data based on the Tweedie distribution

ulcerative_colitis

unifan

Unsupervised cell functional annotation for single-cell RNA-Seq

vcf2maf

Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms

velovi

vision

Signature Analysis and Visualization for Single-Cell RNA-seq

voyager

warp

WDL Analysis Research Pipelines

xcell

Cell types enrichment analysis

yagst