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pinax-news

a simple app for publishing links to news articles on your site

probabilistic-programming-and-bayesian-methods-for-hackers

aka "Bayesian Methods for Hackers": An introduction to Bayesian methods + probabilistic programming with a computation/understanding-first, mathematics-second point of view. All in pure Python ;)

prokka

Rapid prokaryotic genome annotation

pybam

Very simple, pure python, BAM file reader

pychrdraw

Chromosome drawing for comparative genomics

pypeflow

a simple lightweight workflow engine for data analysis scripting

qjobs

qstat wrapper

qstat-pretty

Pretty GridEngine, Torque and Platform LSF status tables

quota-alignment

Guided synteny alignment between duplicated genomes (within specified quota constraint)

racon

Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr.214270.116

readfq

A simple tool to calculate reads number and total base count in FASTQ file

refinery-platform

The Refinery Platform is a data management, analysis and visualization system for bioinformatics and computational biology applications. The platforms consists of three major components: a data repository with rich metadata capabilities, a workflow engine based on the popular Galaxy system, and visualization tools to support the exploration and interpretation of results at all stages of the analysis process.

rnaseq_with_hisat2_stringtie

RNAseq analysis with Hisat2, stringtie, and ballgown

rpi.pihome2.0-gui-frontend

PiHome 2.0 is a RaspberryPI home automation open source project

run_pbjelly

sam2xpkm

Calculate RPKM and FPKM from SAM file

scaffold_summary

A simple program for evaluate the assembly of a give genome.

seq_split

splits a sequence into equal sized chunks with an optional overlapping

seqan

SeqAn's official repository.

sequeloverview

Use Sequel SMRT Link Web Services API to show Statics Information of All Runs

sglink

de novo assembler using simhash graph (sg) for PacBio and Oxford Nanopore data.

smartdenovo

Ultra-fast de novo assembler using long noisy reads

smrt-link

SMRT® Link is the web-based end-to-end workflow manager for the Sequel™ System.

smrtlink-mod

modifyed Pacbio smrtlink UI

smrtlinkr

R package to interface with SMRTLink REST API

somatic_pipeline

肿瘤体细胞突变检测流程（组织、cfDNA均可，需要有对照）

sparc

split_pacbio_bam_by_primer

suffixtree

python implementation of suffix tree, which yields a data structure that can allow substring querying finished in O(n), where n is the length of query string.

superbug

Drug resistance gene database