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http://mirtarbase.mbc.nctu.edu.tw/

Web based manually curated experimentally validated database of microRNA-Target interactions. Collection of MTIs data validated experimentally by reporter assays, western blot, or microarray experiments with overexpression or knockdown of miRNAs.

Proper citation: miRTarBase (RRID:SCR_017355) Copy   

•   Source: SciCrunch Registry

http://geno2mp.gs.washington.edu/Geno2MP/#/

Collection of phenotypic profiles for affected individuals and, for unaffected individuals, the phenotypic profile of their affected. Collaborative, shared resource for the human genetics community.

Proper citation: Geno2MP (RRID:SCR_016872) Copy   

•   Source: SciCrunch Registry

http://diabetes.wisc.edu/index.php

Interactive database of gene expression and diabetes related clinical phenotypes. Allows to search gene expression in tissues as a function of obesity, strain, and age, in a mouse.

Proper citation: Attie Lab Diabetes Database (RRID:SCR_016639) Copy   

•   Source: SciCrunch Registry

http://driverdb.ym.edu.tw/DriverDB/intranet/init.do

A database for cancer driver gene/mutation that incorporates a huge amount of exome-seq data, annotation databases (such as dbSNP, 1000 Genome and Cosmic), and published bioinformatics algorithms dedicated to driver gene/mutation identification.

Proper citation: DriverDB (RRID:SCR_007736) Copy   

•   Source: SciCrunch Registry

http://nectarmutation.org/main

A database and web application to annotate disease-related and functionally important amino acids in human proteins., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: NECTAR (RRID:SCR_007757) Copy   

•   Source: SciCrunch Registry

http://research-public.gene.com/Research/genentech/canpredict/index.html

Web application that uses a combination of computational methods to identify those changes most likely to be cancer-associated.

Proper citation: CanPredict (RRID:SCR_008216) Copy   

•   Source: SciCrunch Registry

http://gaa.mpi-bn.mpg.de/

Data analysis service that allows to process CEL files from Affymetrix, Inc. GeneChip Gene 1.0 ST Arrays to identify alternative splicing.

Proper citation: Gene Array Analyzer (RRID:SCR_008323) Copy   

•   Source: SciCrunch Registry

http://dario.bioinf.uni-leipzig.de/index.py

A free web server for the analysis of short RNAs from high throughput sequencing data.

Proper citation: DARIO (RRID:SCR_008600) Copy   

•   Source: SciCrunch Registry

http://array.mbb.yale.edu/analysis/

A fully integrated platform for processing microarray data.

Proper citation: ExpressYourself (RRID:SCR_008881) Copy   

•   Source: SciCrunch Registry

http://www.rna-seqblog.com/

Blog presenting news and information, and spur discussion about topics related to RNA-Seq.

Proper citation: RNA-Seq Blog (RRID:SCR_010025) Copy   

•   Source: SciCrunch Registry

http://bioinfo1.uni-plovdiv.bg/isomiRex/

A web tool for the identification of microRNAs and their isomiRs, as well as differential expression from NGS datasets.

Proper citation: isomiRex (RRID:SCR_009521) Copy   

•   Source: SciCrunch Registry

http://cbdb.nimh.nih.gov/microsniper/

A web-based application which predicts the impact of a SNP on putative microRNA targets.

Proper citation: MicroSNiPer (RRID:SCR_009880) Copy   

•   Source: SciCrunch Registry

http://centre.bioinformatics.zj.cn/mirtools/

A comprehensive web server developed to allow researchers to comprehensively characterize small RNA transcriptome.

Proper citation: mirTools (RRID:SCR_009701) Copy   

•   Source: SciCrunch Registry

https://github.com/bids-standard/bids-validator

Software validation tool that checks submitted folder structure for compliance to BIDS data standard. Validates Brain Imaging Data Structure.

Proper citation: BIDS Validator (RRID:SCR_017255) Copy   

•   Source: SciCrunch Registry

https://github.com/rrwick/Porechop

Software tool for finding and removing adapters from Oxford Nanopore reads.

Proper citation: Porechop (RRID:SCR_016967) Copy   

•   Source: SciCrunch Registry

https://github.com/voutcn/megahit

Software tool as Next Generation Sequencing assembler. Optimized for metagenomes, but also works well on generic single genome assembly (small or mammalian size) and single cell assembly. Can assemble genome sequences from metagenomic datasets of hundreds of Giga base-pairs in time and memory efficient manner on single server.

Proper citation: MEGAHIT (RRID:SCR_018551) Copy   

•   Source: SciCrunch Registry

http://ccb.jhu.edu/software/stringtie/gff.shtml

Open source software tool to manipulate files in GFF format. Used to convert, sort, filter, transform, or cluster genomic features.

Proper citation: gffread (RRID:SCR_018965) Copy   

•   Source: SciCrunch Registry

https://github.com/brentp/mosdepth

Software command line tool for rapidly calculating genome wide sequencing coverage. Measures depth from BAM or CRAM files at either each nucleotide position in genome or for sets of genomic regions. Used for fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing quick coverage calculation for genomes and exomes.

Proper citation: mosdepth (RRID:SCR_018929) Copy   

•   Source: SciCrunch Registry

http://www.mathcs.emory.edu/panda/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6, 2023. Web-based software program for analyzing phosphorylation antibody arrays. It identifies phosphorylated antibodies in the microarray and statistically quantifies the extent of phosphorylation for these antibodies.

Proper citation: Phosphor Antibody Array Data Analysis (RRID:SCR_000633) Copy   

•   Source: SciCrunch Registry

http://www-personal.umich.edu/~jianghui/rseq/

A software toolkit for RNA sequence data analysis. It contains programs that cover several aspects of RNA-Seq data analysis such as read quality assessment, reference sequence generation, sequence mapping, and gene and isoform expressions estimations.

Proper citation: rSeq (RRID:SCR_000562) Copy   

•   Source: SciCrunch Registry