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http://bioinformatics.research.nicta.com.au/software/rlz/

Optimized relative Lempel-Ziv compression of genomes.

Proper citation: RLZ (RRID:SCR_009420) Copy   

•   Source: SciCrunch Registry

http://ftp://ftp.ieeta.pt/~ap/codecs/GReEn1.tar.gz

A compression tool recently proposed for compressing genome resequencing data using a reference genome sequence., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: GReEn (RRID:SCR_009264) Copy   

•   Source: SciCrunch Registry

https://github.com/lpantano/seqbuster

Software tool for processing and analysis of small RNAs datasets.Reveals ubiquitous miRNA modifications in human embryonic cells.

Proper citation: SeqBuster (RRID:SCR_009616) Copy   

•   Source: SciCrunch Registry

http://omicslab.genetics.ac.cn/ISRNA/

An online toolkit for analyzing high-throughput small RNA sequencing data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: ISRNA (RRID:SCR_009565) Copy   

•   Source: SciCrunch Registry

http://users-mb.au.dk/pmgrp/downloads.php

A pipeline for small RNA-seq data analysis.

Proper citation: shortran (RRID:SCR_009636) 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://genome.sph.umich.edu/wiki/Generic_Exome_Analysis_Plan

Outline of a generic plan for analysis of a whole exome sequencing project.

Proper citation: Generic Exome Analysis Plan (RRID:SCR_009656) Copy   

•   Source: SciCrunch Registry

http://www.labmedmolge.unisa.it/inglese/research/imir

A modular pipeline for comprehensive analysis of smallRNA-Seq data, comprising specific tools for adapter trimming, quality filtering, DE analysis, target prediction by integrating multiple open source modules and resources in an automated workflow.

Proper citation: iMir (RRID:SCR_009496) Copy   

•   Source: SciCrunch Registry

http://www.stanford.edu/group/wonglab/SpliceMap/

A de novo splice junction discovery and alignment tool.

Proper citation: SpliceMap (RRID:SCR_009650) Copy   

•   Source: SciCrunch Registry

https://github.com/bedops/bedops

A suite of tools to address common questions raised in genomic studies - mostly with regard to overlap and proximity relationships between data sets.

Proper citation: BEDOPS (RRID:SCR_012865) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/help/mailing-list/

This mailing list is for announcements about Bioconductor and the availability of new code and questions and answers about problems and solutions using Bioconductor.

Proper citation: Bioconductor mailing list (RRID:SCR_012915) Copy   

•   Source: SciCrunch Registry

https://www.ncbi.nlm.nih.gov/assembly

Database providing information on structure of assembled genomes, assembly names and other meta-data, statistical reports, and links to genomic sequence data. The Archive links the raw sequence information found in the Trace Archive with assembly information found in publicly available sequence repositories (GenBank/EMBL/DDBJ).

Proper citation: NCBI Assembly Archive Viewer (RRID:SCR_012917) Copy   

•   Source: SciCrunch Registry

http://bioinf.wehi.edu.au/featureCounts/

A read summarization program, which counts mapped reads for the genomic features such as genes and exons.

Proper citation: featureCounts (RRID:SCR_012919) Copy   

•   Source: SciCrunch Registry

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

Biclustering Analysis and Results Exploration.

Proper citation: BicARE (RRID:SCR_012881) Copy   

•   Source: SciCrunch Registry

http://bioinfo2.ugr.es/NGSmethDB/

A dedicated database for the storage, browsing and data mining of whole-genome, single-base-pair resolution methylomes.

Proper citation: NGSmethDB (RRID:SCR_012847) Copy   

•   Source: SciCrunch Registry

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

Function for differentially methylated regions (DMR) detection that is a part of the charm package in R/Bioconductor.

Proper citation: dmrFinder (RRID:SCR_012853) Copy   

•   Source: SciCrunch Registry

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

Software package that includes functions to retrieve the sequences around the peak, obtain enriched Gene Ontology terms, find the nearest gene, exon, miRNA or custom features such as most conserved elements.

Proper citation: ChIPpeakAnno (RRID:SCR_012828) Copy   

•   Source: SciCrunch Registry

http://mitobreak.portugene.com/cgi-bin/Mitobreak_home.cgi

Database with curated datasets of mitochondrial DNA (mtDNA) rearrangements. Users may submit new mtDNA rearrangements.

Proper citation: MitoBreak (RRID:SCR_012949) Copy   

•   Source: SciCrunch Registry

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

Collection of techniques to remove inter-study bias when combining gene expression data originating from different studies.

Proper citation: inSilicoMerging (RRID:SCR_012829) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/release/bioc/html/DEXSeq.html

Software package focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results.

Proper citation: DEXSeq (RRID:SCR_012823) Copy   

•   Source: SciCrunch Registry