csb5 Goto Github PK

16s-arxiv-1210.3464

Auxiliary scripts for Ong et al. (2013): Species Identification and Unbiased Profiling of Complex Microbial Communities Using Shotgun Illumina Sequencing of 16S rRNA Amplicon Sequences

2015-do-hrsv

Supplementary Data for Do et al. (2015)

ad-caregiver-manuscript

Files and scripts to generate figures for the manuscript titled "Shared signatures and divergence in skin microbiomes of children with atopic dermatitis and their adult caregivers"

atminter

SVM/regex abstract parser for identification of microbial interactions

bamsurgeon

tools for adding mutations to existing .bam files, used for testing mutation callers

basespace-bacterial-lofreq

Bacterial LoFreq Wrapper for Basespace

beem

BEEM: Estimating Lotka-Volterra models from time-course microbiome sequencing data

beem-static

BEEM-Static: An R package for inferring microbial interactions based on generalized Lotka-Volterra models

cadrres

Cancer Drug Response prediction using a Recommender System

cadrres-sc

CaDRReS-Sc is a framework for analyzing drug response heterogeneity based on single-cell RNA-seq data

candida_auris_cladevi

WGS analysis for Candida auris

cpe-microbiome

csb5.github.io

github pages for csb5

decont

Decontaminate FastQ files

driver-benchmarking

Pipeline for mutation benchmarking of various softwares.

driver_evaluation

drug_response_consistency

Preliminary study of consistency among public cancer drug response datasets

edda

Power Your Design

food_centre_microbiome

City-wide metagenomic surveillance of food centres reveals location-specific microbial signatures and enrichment of antibiotic resistance genes

germs_16s_pipeline

Pipeline for Illumina shotgun sequencing of 16S rRNA amplicon sequences

giraf

Robust, Computational Identification of Influenza Reassortments via Graph Mining

hospital_microbiome

hospital_microbiome_explorer

inc-seq

INC-Seq: Accurate single molecule reads using nanopore sequencing

lofreq

LoFreq Star: Sensitive variant calling from sequencing data

metagenn

MetageNN is a proof of concept neural network used to obtain a memory-efficient taxonomic classifier robust to sequencing errors and missing genomes

misc-scripts

Miscellaneous scripts

nanosim

Nanopore sequence read simulator

oncoimpact

Cancer-omics Data Integration

opera-ms

OPERA-MS - Hybrid Metagenomic Assembler