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http://sourceforge.net/projects/mirseq/files/

An R/Bioconductor based workflow for novel miRNA prediction from deep sequencing data.

Proper citation: miRSeqNovel (RRID:SCR_013257) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/dynamicprog/

A model-based statistical methods for base calling in Illumina''s next-generation sequencing platforms.

Proper citation: DynamicProg (RRID:SCR_013217) Copy   

•   Source: SciCrunch Registry
  

http://beads.sourceforge.net/

Software for a normalization scheme that corrects nucleotide composition bias, mappability variations and differential local DNA structural effects in deep sequencing data.

Proper citation: BEADS (RRID:SCR_013229) Copy   

•   Source: SciCrunch Registry
  

http://geckoe.sourceforge.net/

A complete, high-capacity centralized gene expression analysis system, developed in response to the needs of a distributed user community.

Proper citation: Gecko (RRID:SCR_009001) Copy   

•   Source: SciCrunch Registry
  

http://scalce.sourceforge.net/Home

A FASTQ compression tool that uses locally consistent parsing to obtain better compression rate.

Proper citation: SCALCE (RRID:SCR_009658) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/apps/mediawiki/cdao/

A formalization of concepts and relations relevant to evolutionary comparative analysis, such as phylogenetic trees, OTUs (operational taxonomic units) and compared characters (including molecular characters as well as other types). CDAO is being developed by scientists in biology, evolution, and computer science

Proper citation: Comparative Data Analysis Ontology (RRID:SCR_010297) Copy   

•   Source: SciCrunch Registry
  

http://htsvipr.sourceforge.net/

A software program to screen for sequence variants (SNPs, deletions) in sequence data generated by high-throughput-sequencing platforms.

Proper citation: vipR (RRID:SCR_010685) Copy   

•   Source: SciCrunch Registry
  

http://contra-cnv.sourceforge.net/

A tool for copy number variation (CNV) detection for targeted resequencing data such as those from whole-exome capture data.

Proper citation: CONTRA (RRID:SCR_010814) Copy   

•   Source: SciCrunch Registry
  

http://svdetect.sourceforge.net/Site/Home.html

Software application for the isolation and the type prediction of intra- and inter-chromosomal rearrangements from paired-end/mate-pair sequencing data provided by the high-throughput sequencing technologies. This tool aims to identify structural variations with both clustering and sliding-window strategies, and helping in their visualization at the genome scale. It is compatible with SOLiD and Illumina (>=1.3) reads.

Proper citation: SVDetect (RRID:SCR_010812) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/apps/mediawiki/vancouvershortr/index.php?title=FindPeaks

Software application that can be used for converting Eland, Maq (.map), BED or other files into WIG files and identifying areas of enrichment (ChIP-Seq analysis).

Proper citation: FindPeaks (RRID:SCR_010857) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/apps/mediawiki/wgs-assembler/index.php?title=Main_Page

A de novo whole-genome shotgun (WGS) DNA sequence assembler.

Proper citation: Celera assembler (RRID:SCR_010750) Copy   

•   Source: SciCrunch Registry
  

https://compbio.dfci.harvard.edu/predictivenetworks//

A flexible, open-source, web-based application and data services framework that enables the integration, navigation, visualization and analysis of gene interaction networks. The primary goal of PN is to allow biomedical researchers to evaluate experimentally derived gene lists in the context of large-scale gene interaction networks. The PN analytical pipeline involves two key steps. The first is the collection of a comprehensive set of known gene interactions derived from a variety of publicly available sources. The second is to use these ''known'' interactions together with gene expression data to infer robust gene networks. The regression-based network inference algorithm creates a graph of gene interactions in which cycles may be present (but no self-loops). Based on information-theoretic techniques, a causal gene interaction network is inferred from both prior knowledge (interactions extracted from biomedical literature and structured biological databases) and gene expression data. A prediction model is fitted for each gene, given its parents, enabling assessment of the predictive ability of the network model.

Proper citation: Predictive Networks (RRID:SCR_006110) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/bless-ec/

Software tool for Bloom-filter-based error correction for next-generation sequencing (NGS) reads. The algorithm produces accurate correction results with much less memory.

Proper citation: BLESS (RRID:SCR_005963) Copy   

•   Source: SciCrunch Registry
  

http://buridan.sourceforge.net/

Open source software written in R that tracks a single animal walking in a homogenous environment (Buritrack) and analyzes its trajectory. It extracts eleven metrics and includes correlation analyses and a Principal Components Analysis (PCA). It was designed to be easily customized to personal requirements. In combination with inexpensive hardware, these tools can readily be used for teaching and research purposes. Buritrack is a program to track individual Drosophila fruit flies online with any camera as they walk in Buridan's paradigm. The program extracts the coordinate locations of the fly and stores them in a text file.

Proper citation: Centroid Trajectory Analysis (RRID:SCR_006331) Copy   

•   Source: SciCrunch Registry
  

http://seqbarracuda.sourceforge.net/

A sequence mapping software that utilizes the massive parallelism of graphics processing units to accelerate the inexact alignment of short sequence reads to a particular location on a reference genome. It can align a paired-end library containing 14 million pairs of 76bp reads to the Human genome in about 27 minutes (from fastq files to SAM alignment) using a ��380 NVIDIA Geforce GTX 680*. The alignment throughput can be boosted further by using multiple GPUs (up to 8) at the same time. Being based on BWA (http://bio-bwa.sf.net) from the Sanger Institute, BarraCUDA delivers a high level of alignment fidelity and is comparable to other mainstream alignment programs. It can perform gapped alignment with gap extensions, in order to minimise the number of false variant calls in re-sequencing studies.

Proper citation: BarraCUDA (RRID:SCR_006881) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/polgui/

An interface between MATLAB and the Polhemus Fastrak digitizer used to digitize fiducial locations and scalp EEG electrode locations. There are 5 versions all of which work under MATLAB R14 (on both linux and windows platforms), # polgui_ver1_r14 : works with 1 receiver (stylus pen) # polgui_ver2_r14 : works with 2 receivers (including the pen) # polgui_ver3_r14 : works with 3 receivers(including the pen) # polgui_ver4_r14 : works with 4 receivers (including the pen) # polgui_ver5_r14 : Generic version which works with 1/2/3/4 receivers (WARNING: Ver 5 might be buggy; not fully tested) Requirements: MATLAB R14 (Linux/Windows)

Proper citation: POLGUI - Matlab Polhemus Interface (RRID:SCR_006752) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/mubiomics/

A set of scripts (mostly python) for processing reads generated by the Roche 454 or Illumina next-gen sequencing platforms. Included are quality control, read demultiplexing and microbiome characterisation scripts for use with usearch, pplacer and RDP classifier.

Proper citation: mubiomics (RRID:SCR_006785) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/splicegrapher/

Software that predicts alternative splicing patterns and produces splice graphs that capture in a single structure the ways a gene''s exons may be assembled. It enhances gene models using evidence from next-generation sequencing and EST alignments.

Proper citation: SpliceGrapher (RRID:SCR_006657) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/qudaich/

A software package for local sequence alignment for next-generation sequencing (NGS) data. It generates the pairwise local alignments between a query dataset against a database. The main design purpose of qudaich is to focus on datasets from next generation sequencing. These the datasets generally have hundreds of thousand sequences or more, and so, the input database should contain large number of sequences. Qudaich is flexible and its algorithmic structure imposes no restriction on the absolute limit of the acceptable read length, but the current version of qudaich allow read length <2000 bp. Qudaich can be used to align DNA, translated DNA and protein sequences.

Proper citation: Qudaich (RRID:SCR_006775) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/gbsbarcode/

PERL script used to split barcode of Illumina sequencing data created by GBS protocol (www.maizegenetics.net). The barcode has variable size. Paired-end reads are supported.

Proper citation: GBS barcode splitter (RRID:SCR_006799) Copy   

•   Source: SciCrunch Registry