rsem

RNA-Seq by Expectation-Maximization

RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data. The RSEM package provides an user-friendly interface, supports threads for parallel computation of the EM algorithm, single-end and paired-end read data, quality scores, variable-length reads and RSPD estimation. In addition, it provides posterior mean and 95% credibility interval estimates for expression levels. For visualization, It can generate BAM and Wiggle files in both transcript-coordinate and genomic-coordinate. Genomic-coordinate files can be visualized by both UCSC Genome browser and Broad Institute’s Integrative Genomics Viewer (IGV). Transcript-coordinate files can be visualized by IGV. RSEM also has its own scripts to generate transcript read depth plots in pdf format. The unique feature of RSEM is, the read depth plots can be stacked, with read depth contributed to unique reads shown in black and contributed to multi-reads shown in red. In addition, models learned from data can also be visualized. Last but not least, RSEM contains a simulator.

node-ace-builds

standalone code editor, written in JavaScript

Ace (Ajax.org Cloud9 Editor) aims to provide an in-browser editing experience that compares favourably with native editors such as TextMate, Vim or Eclipse.

r-bioc-deseq2

R package for RNA-Seq Differential Expression Analysis

Differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.

python3-exchangelib

Client for Microsoft Exchange Web Services (Python3 version)

This module provides an well-performing, well-behaving, platform-independent and simple interface for communicating with a Microsoft Exchange 2007-2016 Server or Office365 using Exchange Web Services (EWS). It currently implements autodiscover, and functions for searching, creating, updating, deleting, exporting and uploading calendar, mailbox, task, contact and distribution list items.

sagan-rules

Real-time System & Event Log Monitoring System [rules]

Sagan is a multi-threaded, real time system- and event-log monitoring system, but with a twist. Sagan uses a “Snort” like rule set for detecting malicious events happening on your network and/or computer systems. If Sagan detects a potentially bad event, that event can be stored to a Snort database (MySQL/PostgreSQL), send it to a SIEM tool like Prelude, or send an email.

python3-django-pgschemas

Django multi-tenancy using PostgreSQL schemas (Python3 version)

This app uses PostgreSQL schemas to support data multi-tenancy in a single Django project. It is a fork of django-tenants with some conceptual changes: