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aml2019

The following code accompanies a manuscript combining single-cell RNA-sequencing and genotyping to analyze cellular hierarchies in acute myeloid leukemia (AML). The final scripts are being generated and will be uploaded shortly.

cb_sniffer

mutation(barcode) caller for 10x single cell data

chembl_tools

Small scripts to make the most of the ChEMBL API

clusterprofiler

:bar_chart:statistical analysis and visualization of functional profiles for genes and gene clusters

conics

CONICS: COpy-Number analysis In single-Cell RNA-Sequencing

datasciencecoursera

dropest

Pipeline for initial analysis of droplet-based single-cell RNA-seq data

evip2

Expression-based variant impact phenotyping

fgsea

Fast Gene Set Enrichment Analysis

gateid

Cell type purification by single-cell transcriptome-trained sorting

genome-assembly

incubator-singa

Mirror of Apache Singa (Incubating)

kallisto

Near-optimal RNA-Seq quantification

liger

Lightweight Iterative Gene set Enrichment in R

mast

Tools and methods for analysis of single cell assay data in R

monocle-release

pandas-tutorial

适合初级到中级晋升者，有了体系之后就看熟练度了。

pandoc-crossref

pandoc filter for cross-references

popscle

A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and auxilary tools

sccancer

A package for automated processing of single cell RNA-seq data in cancer

scde

R package for analyzing single-cell RNA-seq data

scrna-seq-tcc-prep

Preprocessing of single-cell RNA-Seq data for input to kallisto

scrna.seq.course

Analysis of single cell RNA-seq data course

scrna_mutations

Supplementary data for Petti, et al 2019 scRNA mutation publication

seurat

R toolkit for single cell genomics

sexlinked

Code to replicate results of "Systematic Rational Identification of Sex-Linked Molecular Alterations and Therapies in Cancer"

single_cell_pipeline

Single Cell Analysis Automated Workflow

singler

SingleR: Single-cell RNA-seq cell types Recognition

sleuth

Differential analysis of RNA-Seq

umi-tools

Tools for handling Unique Molecular Identifiers in NGS data sets