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http://tron-mainz.de/tron-facilities/computational-medicine/seq2hla/

Software for obtaining an individualXs HLA class I and II type and expression using standard NGS (Next-generation sequencing) RNA-Seq data. It comprises mapping RNA-Seq reads against a reference database of HLA alleles, determining and reporting HLA type, confidence score and locus-specific expression level.

Proper citation: seq2HLA (RRID:SCR_001199) Copy   

•   Source: SciCrunch Registry

http://sequedex.lanl.gov/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025.Software to classify the function and phylogeny of reads as short as 30 bp. It is flexible, which can utilize multiple data modules and downstream analysis scripts. It is fast, reading in signature lists of 5-500 million peptide signatures in 1-15 minutes, and subsequently processes genomic fragments at the rate of 6 Gbp/hr. It parallelizes without significant increase in memory requirements until I/O bound on multiple input files; parallelization works well on 64 processors.

Proper citation: Sequedex (RRID:SCR_001233) Copy   

•   Source: SciCrunch Registry

http://english.pku.edu.cn/

Chinese research university in Beijing, China that offers undergraduate and graduate degree programs in pure and applied sciences, social sciences and humanities, and sciences of management and education.

Proper citation: Peking University; Beijing; China (RRID:SCR_001193) Copy   

•   Source: SciCrunch Registry

http://www.bioinformatics.org/peakanalyzer/wiki/

A set of standalone software programs for the automated processing of any genomic loci, with an emphasis on datasets consisting of ChIP-derived signal peaks. The software is able to identify individual binding / modification sites from enrichment loci, retrieve peak region sequences for motif discovery, and integrate experimental data with different classes of annotated elements throughout the genome. PeakAnalyzer requires a peak file and a feature annotation file in BED or GTF format. Complete annotation files for the current builds of the human (HG19) and mouse (MM9) genomes are provided with the software distribution.

Proper citation: PeakAnalyzer (RRID:SCR_001194) Copy   

•   Source: SciCrunch Registry

http://sv.gersteinlab.org/breakseq/

Software for scanning reads from short-read sequenced genomes against a human breakpoint library to accurately identify structural variants (SVs). The library of breakpoints at nucleotide resolution were assembled from collating and standardizing ~2,000 published structural variants (SVs). For each breakpoint, its ancestral state (through comparison to primate genomes) was inferred and its mechanism of formation (e.g., nonallelic homologous recombination, NAHR).

Proper citation: BreakSeq (RRID:SCR_001186) Copy   

•   Source: SciCrunch Registry

http://thirdreviewer.com/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 11, 2017. The Third Reviewer is a forum for scientists to share opinions about recently published research. Currently both microbiology and neuroscience papers in different journals are included. Third Reviewer allows anonymous commenting and provides a centralized location for commentary on papers from 11 major neuroscience venues.

Proper citation: Third Reviewer (RRID:SCR_001187) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/categoryCompare.html

A software package for meta-analysis of high-throughput experiments using feature annotations. It calculates significant annotations (categories) in each of two (or more) feature (i.e. gene) lists, determines the overlap between the annotations, and returns graphical and tabular data about the significant annotations and which combinations of feature lists the annotations were found to be significant. Interactive exploration is facilitated through the use of RCytoscape (heavily suggested).

Proper citation: categoryCompare (RRID:SCR_001223) Copy   

•   Source: SciCrunch Registry

http://www.covance.com/

A contract research organization providing drug development and animal testing services. Under the name Covance Research Products Inc., based in Denver, Pennsylvania, the company also deals in the import, breeding and sale of laboratory animals. It breeds dogs, rabbits, guinea pigs, non-human primates, and pigs, and runs the largest non-human primate laboratory in Germany. (Wikipedia)

Proper citation: Covance (RRID:SCR_001224) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/MergeMaid.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. R extension whose functions are intended for cross-study comparison of gene expression array data. Required from the user is gene expression matrices, their corresponding gene-id vectors and other useful information, and they could be "list", "matrix", or "ExpressionSet". The main function is "mergeExprs" which transforms the input objects into data in the merged format, such that common genes in different datasets can be easily found. And the function "intcor" calculate the correlation coefficients. Other functions use the output from "modelOutcome" to graphically display the results and cross-validate associations of gene expression data with survival.

Proper citation: MergeMaid (RRID:SCR_001221) Copy   

•   Source: SciCrunch Registry

http://www.webcitation.org/getfile?fileid=05c70eb653a3b267453212d27dd8ac8c211c0f96

Application that provides users an interface to design analysis protocols combining one or more normalization and filtering steps. In this way, data from many individual hybridizations can be treated in a uniform and reproducible manner.

Proper citation: Microarray Data Analysis System (RRID:SCR_001218) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/globaltest.html

A software package that tests groups of covariates (or features) for association with a response variable. The package implements the test with diagnostic plots and multiple testing utilities, along with several functions to facilitate the use of this test for gene set testing of GO and KEGG terms.

Proper citation: globaltest (RRID:SCR_001256) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/snpStats.html

Software for classes and statistical methods for large single nucleotide polymorphism (SNP) association studies.

Proper citation: snpStats: SnpMatrix and XSnpMatrix classes and methods (RRID:SCR_001249) Copy   

•   Source: SciCrunch Registry

https://sites.google.com/site/vibansal/software/picall

Software to detect short insertion / deletion variants (and SNPs) from population sequence data, i.e. sequence reads generated from a population of individuals. It uses a probabilistic model to utilize sequence reads from a population of individuals to automatically account for context-specific sequencing errors associated with indels. piCALL is implemented in C for use on Linux platforms and can be applied to sequence data from different sequencing platforms. However, the method requires each individual in a dataset to be sequenced using the same platform. The reads for each individual should be aligned to the same reference genome sequence. Note that the program will not be able to call indels from individual sequence datasets or data from a small number of individuals.

Proper citation: piCALL (RRID:SCR_001242) Copy   

•   Source: SciCrunch Registry

http://ginolhac.github.io/mapDamage/

Software for tracking and quantifying DNA damage patterns among ancient DNA sequencing reads generated by Next-Generation Sequencing platforms.

Proper citation: mapDamage (RRID:SCR_001240) Copy   

•   Source: SciCrunch Registry

http://sun.aei.polsl.pl/kmc/

Software utility for counting k-mers (sequences of consecutive k symbols) in a set of reads from genome sequencing projects. It scans the raw reads and produces a compact representation of all non-unique reads accompanied with number of their occurrences. The algorithm implemented makes use mostly of disk space rather than RAM, which allows to use KMC even on rather typical personal computers.

Proper citation: KMC (RRID:SCR_001245) Copy   

•   Source: SciCrunch Registry

http://minia.genouest.org/dsk/

A k-mer counting software that can count k-mers of large Illumina datasets on laptops and desktop computers.

Proper citation: DSK (RRID:SCR_001246) Copy   

•   Source: SciCrunch Registry

https://gitlab.sib.swiss/EPD/chipseq

Set of software modules for performing common ChIP-seq data analysis tasks across the whole genome, including positional correlation analysis, peak detection, and genome partitioning into signal-rich and signal-poor regions. The tools are designed to be simple, fast and highly modular. Each program carries out a well-defined data processing procedure that can potentially fit into a pipeline framework. ChIP-Seq is also freely available on a Web interface.

Proper citation: ChIP-seq (RRID:SCR_001237) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages//2.12/bioc/html/exomeCopy.html

Software package for detection of copy number variants (CNV) from exome sequencing samples, including unpaired samples. The package implements a hidden Markov model which uses positional covariates, such as background read depth and GC-content, to simultaneously normalize and segment the samples into regions of constant copy count.

Proper citation: exomeCopy (RRID:SCR_001276) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.14/bioc/html/SMAP.html

Software package providing functions and classes for DNA copy number profiling of array-CGH data.

Proper citation: SMAP (RRID:SCR_001270) Copy   

•   Source: SciCrunch Registry

http://lamp.icsi.berkeley.edu/lamp/

A software package for the inference of locus-specific ancestry in recently admixed populations. LAMP-LD takes the genotypes of admixed individuals as well as reference haplotype panels approximating the mixing ancestral populations, and outputs the estimated number of alleles from each ancestry in each locus for each individual. The LAMP-LD package also includes the program LAMP-HAP, which processes haplotype data when high-quality phasing is available, and utilizes trio nuclear family designs to improve estimation accuracy. LAMP-LD is based on a window-based processing combined within a hierarchical Hidden Markov Model. It can process 2,3 or 5 mixing populations, and its short per-sample processing time makes it suitable for analyzing large datasets of dense SNP panels. The original program LAMP does not use the LD and therefore is not as accurate, but it is useful in cases where the SNP density is not high enough or when the ancestral haplotypes are unkown.

Proper citation: Local Ancestry in adMixed Populations (RRID:SCR_001258) Copy   

•   Source: SciCrunch Registry