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speedseq

A flexible framework for rapid genome analysis and interpretation

sqlcipher

SQLCipher is an SQLite extension that provides 256 bit AES encryption of database files.

squid

SQUID detects both fusion-gene and non-fusion-gene structural variations from RNA-seq data

sra-tools

SRA Tools

sratoolkit

SRAToolkit has been REPLACED - see README

stampedeblast

Running BLAST on local file system: XSEDE-Stampede

standard-raxml

standards2

star

RNA-seq aligner

star-fusion-tutorial

Tutorial for STAR-Fusion, FusionInspector, and de novo reconstruction of fusion transcripts using Trinity

statgen-esalq

The web page of the Statistical Genetics Lab (ESALQ/USP)

structural-information-minimisation

Code of structural entropy minimisation for TAD identification of Hic matrix

supernova

10x Genomics Linked-Read Diploid De Novo Assembler

superputty

The SuperPuTTY Window Manager for putty sessions

svmine

swirl

:cyclone: Learn R, in R.

swirl_courses

:mortar_board: A collection of interactive courses for the swirl R package.

tablemaker

Preprocessing software for prepping Cufflinks output for Ballgown

tadbit

TADbit is a complete Python library to deal with all steps to analyze, model and explore 3C-based data. With TADbit the user can map FASTQ files to obtain raw interaction binned matrices (Hi-C like matrices), normalize and correct interaction matrices, identify and compare the so-called Topologically Associating Domains (TADs), build 3D models from the interaction matrices, and finally, extract structural properties from the models. TADbit is complemented by TADkit for visualizing 3D models

tag-based_rnaseq

Cost-efficient genome-wide gene expression profiling

target_prediction

taxonkit

A cross-platform and Efficient NCBI Taxonomy Toolkit

tbtools

GUI/CommandLine Tool Box for biologistists to utilize NGS data.

tensorflow

Computation using data flow graphs for scalable machine learning

tentakel

test_io

test_io1

tigervnc

High performance, multi-platform VNC client and server

tiledb

TileDB

tmux

tmux source code

tmuxinator

Manage complex tmux sessions easily