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scmatch

scMatch: a single-cell gene expression profile annotation tool using reference datasets

scrna.seq.course

Analysis of single cell RNA-seq data course

scrnaseq_benchmark

Bench-marking classification tools for scRNA-seq data

scrnaseq_cell_cluster_labeling

Scripts to run and benchmark scRNA-seq cell cluster labeling methods

sequencing-projects

seurat

R toolkit for single cell genomics

shiny-app-user-authentication

A template for a user authentication interface in RShiny

shiny-examples

shinyproxy-config-examples

Configuration examples for ShinyProxy

shinyproxy-lbi

docker image and Dockerfile build folder for LBI shinyproxy test

shiny_password

Template for making a login screen for R Shiny web apps

simupop

A general-purpose forward-time population genetics simulation environment.

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"

singler

Clone of the Bioconductor repository for the SingleR package.

skylab

Secondary analysis pipelines

snapatac

Analysis Pipeline for Single Cell ATAC-seq

spliceai

A deep learning-based tool to identify splice variants

sponge

Sparse Partial correlation ON Gene Expression - an R package for fast and robust ceRNA network inference

sscclust

simpler single cell RNAseq data clustering

stat-cookbook

:orange_book: The probability and statistics cookbook

stat-learning

Notes and exercise attempts for "An Introduction to Statistical Learning"

stat479-machine-learning-fs18

Course material for STAT 479: Machine Learning (FS 2018) at University Wisconsin-Madison

systemsgenetics

Generic Java genotype reader / writer, QTL mapping software, Strand alignment tool

targeted_transcriptomics

Mair and Erickson, A targeted multi-omic analysis approach measures protein expression and low abundance transcripts on the single cell level

tcga2bed

The Cancer Genome Atlas Data Extraction and Conversion Tool

tcgaome

tcga_rnaseq_clinical

tdm

R package for normalizing RNA-seq data to make them comparable to microarray data.

teachingmaterial

RNA-seq data analysis practical

the-broad-institute-single-cell-rna-seq-data-set

Visualize cancer genomes with FAIR single-cell RNA-seq data