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analysis-scripts

aneu-analysis

archr

ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)

assignments

asteroidsgame

cacoa

Single-cell Case Control Analysis

catalyst

Cytometry dATa anALYsis Tools

chemotaxis

cite-seq-count

A tool that allows to get UMI counts from a single cell protein assay

cpecan

C + python code for pairwise multiple sequence alignment, pulling out this functionality from the Cactus alignment program.

dice

doubletfinder

R package for detecting doublets in single-cell RNA sequencing data

dynast-release

Inclusive and efficient quantification of labeling and splicing RNAs for time-resolved metabolic labeling based scRNA-seq experiments

epc

Ensemble Pathogenicity Classifier

escape

Ensemble Single Cell Analysis Pipeline: ensemble method to remove ambient RNA, empty droplets, doublets, and imputation.

ewce

Expression Weighted Celltype Enrichment. See the package website for up-to-date instructions on usage.

fall-17-scml-competition

SCML Fall 2017 Competition: Can machines learn how the mouse sees?

freebarcodes

FREE Divergence Error-Correcting DNA Barcodes

geometrichashing

Global, Highly Specific and Fast Filtering of Alignment Seeds

group_clone

Computational strategy for identifying clonal cells in single-cell CRISPR screen.

guessinghexmips

hdwgcna

High dimensional weighted gene co-expression network analysis

integrative-spatiotemporal-analysis-of-human-microglia-scripts

knn

lightning

Sample code for Lowell High School Lightning Assignment

lps

Locally Purified States

minimap2-acceleration

Hardware Acceleration of Long Read Pairwise Overlapping in Genome Sequencing: Open Source Repository

muscat

Multi-sample multi-group scRNA-seq analysis tools

nanosensus

nextclone

Nextflow pipeline for extracting and counting clonal barcodes