yuanjingnan Goto Github PK

16s-rrna-gene-analysis-using-qiime2

QIIME2 worklflow. From raw data to a feature table.

2020plus

Classifies genes as an oncogene, tumor suppressor gene, or as a non-driver gene by using Random Forests

ampliconarchitect

AmpliconArchitect (AA) is a tool to identify one or more connected genomic regions which have simultaneous copy number amplification and elucidates the architecture of the amplicon. In the current version, AA takes as input next generation sequencing reads (paired-end Illumina reads) mapped to the hg19/GRCh37 reference sequence and one or more regions of interest. Please "watch" this repository for improvements in runtime, accuracy and annotations for GRCh38 human reference genome coming up soon.

ascat

ASCAT copy number R package

awesome-single-cell

List of software packages for single-cell data analysis, including RNA-seq, ATAC-seq, etc.

bamixchecker

BAMixChecker: A fast and efficient tool for sample matching checkup

basic-knowledge

bitmapperbs

BitMapperBS: a fast and accurate read aligner for whole-genome bisulfite sequencing

bms038_analysis

Code and additional processed data for manuscript "Tumor and Microenvironment Evolution during Immunotherapy with Nivolumab"; see for manuscript https://doi.org/10.1016/j.cell.2017.09.028 See also http://www.ioexplorer.org for interactive visuallization

bseqsc

Bulk-Sequence Single-Cell Gene Expression Deconvolution Pipeline

c3po_polygenic

Basic linear polygenic risk score to predict protein levels in CPTAC

ccle_heterogeneity

cellbender

CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.

cg

CG - cancer genomics pipeline

cnapp

CNApp represents the first web tool to perform a comprehensive and integrative analysis of copy number alterations (CNAs) in a user-friendly interface. The software uses segmented data from either aCGH, SNP-array, whole-exome sequencing or whole-genome sequencing to assess sample profiles and CNA levels, establishing associations with molecular and clinical features. CNApp has three main sections: Re-Seg & Score, Region profile and Classifier model

csv2xlsx-student

Convertor for results of student's simulations in CSV to XLSX.

d-o-connor

dbscan-swa

denv

A part of R codes used for "Principal Components Analysis Based Unsupervised Feature Extraction Applied to Gene Expression Analysis of Blood from Dengue Haemorrhagic Fever Patients" https://www.nature.com/articles/srep44016

digitalcytometry_emt_2020

R scripts and supporting files for creating EMT state metrics for bulk RNAseq profiling of tissue samples

discvrseq

A collection of command line tools for working with sequencing data

dna-seq-analysis

DNA sequencing analysis notes from Ming Tang

emt_dynamics

Scripts used for "Comparing transcriptional dynamics of the epithelial-mesenchymal transition"

emt_prognosis-master

escc-code

facets-suite

Utility functions for FACETS

fusioncatcher

Finder of Somatic Fusion Genes in RNA-seq data

fxtools

FxTools: a comprehensive toolkit for FASTA and FASTQ file manipulation

gbmap

Code used to create the core and extended GBmap, including downstream analyses (cell-cell interactions, spatial transcriptomics deconvolution) and how to produce the figures.

gefpy