Software Updates

SvABA

Structural variation and indel analysis by assembly.

Scallop

Scallop is an accurate reference-based transcript assembler.

R-pkgs-Biogrids

contains common and requested R packages for BIOGRIDS. This title is dependent on R.

LDSC

a command line tool for estimating heritability and genetic correlation from GWAS summary statistics. ldsc also computes LD Scores.

PyTorch

an open source deep learning platform that provides a seamless path from research prototyping to production deployment.

PEER

a collection of Bayesian approaches to infer hidden determinants and their effects from gene expression profiles using factor analysis methods.

Python

a general-purpose, interpreted, object oriented, high-level dynamic programming language that emphasizes code readability. Its syntax allows programmers to express concepts in fewer lines of code than in C++ or Java, thus allowing programmers to work more quickly and integrate their systems more effectively.

CUDA

redistributable software libraries to support CUDA applications for Linux.

PyMOL Open Source

open source version of the widely used molecular visualization package developed by Warren DeLano.

TelSeq

a software that estimates telomere length from whole genome sequencing data (BAMs).

assembly-stats

Get assembly statistics from FASTA and FASTQ files.

CRISPRitz

a software package containing 5 different tools dedicated to perform predictive analysis and result assessement on CRISPR/Cas experiments.

medaka

a tool to create consensus sequences and variant calls from nanopore sequencing data.

Hopla

Hopla enables classic genomic single, duo, trio, etc., analysis, by studying a single (multisample) vcf-file, eventually generating interactive visualizations.

csvtk

a set of tools for manipulation of CSV/TSV files. It is convenient for rapid data investigation and integration into analysis pipelines.

STAR-Fusion

a component of the Trinity Cancer Transcriptome Analysis Toolkit (CTAT), STAR-Fusion uses the STAR aligner to identify candidate fusion transcripts supported by Illumina reads. STAR-Fusion further processes the output generated by the STAR aligner to map junction reads and spanning reads to a reference annotation set.

Fast Data Transfer - FDT

FDT is an Application for Efficient Data Transfers which is capable of reading and writing at disk speed over wide area networks (with standard TCP). It is written in Java, runs an all major platforms and it is easy to use.

SAMtools

(Sequence Alignment/Map) a generic format for storing large nucleotide sequence alignments that provides various utilities for manipulating alignments, including sorting, merging, indexing and generating alignments in a per-position format.

MAPS

MAPS (Model-based Analysis of PLAC-Seq data) pipeline is a a set of multiple scripts used to analyze PLAC-Seq and HiChIP data.

NanoPlot

Plotting tool for long read sequencing data and alignments.

xterm

a terminal emulator for the X Window System that provides DEC VT102 and Tektronix 4014 compatible terminals for programs that can't use the window system directly.