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: