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https://github.com/Oshlack/necklace/wiki

Software that combines reference and assembled transcriptomes for RNA-Seq analysis. It replaces many manual steps in the pipeline of RNA-Seq analyses involving species with incomplete genome or annotations.

Proper citation: Necklace (RRID:SCR_016103) Copy   

•   Source: SciCrunch Registry
  

http://www2.mrc-lmb.cam.ac.uk/relion

Software for determination of cryo-EM structures. It employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy.

Proper citation: RELION (RRID:SCR_016274) Copy   

•   Source: SciCrunch Registry
  

http://zzlab.net/blink/index.html

Software for next level of genome wide association studies with both individuals and markers in millions. The method releases the requirement that causative genes are evenly distributed on genome and consequently boosts statistical power.

Proper citation: BLINK (RRID:SCR_016288) Copy   

•   Source: SciCrunch Registry
  

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

Software tool for automated meta-analysis of mass and flow cytometry data. Provides functions for preprocessing, automated gating and meta-analysis of cytometry data and collection of cytometry data from the ImmPort database.

Proper citation: MetaCyto (RRID:SCR_016415) Copy   

•   Source: SciCrunch Registry
  

https://github.com/sblanck/smagexp

Software toolkit for transcriptomics data meta-analysis. It integrates metaMA and metaRNAseq packages into Galaxy, carries out meta-analysis of gene expression data, handles microarray data from Gene Expression Omnibus (GEO) database, and more.

Proper citation: SMAGEXP (RRID:SCR_016360) Copy   

•   Source: SciCrunch Registry
  

https://omictools.com/fluxmodecalculator-tool

Software for performing flux mode analysis in stoichiometric models. FluxModeCalculator enables large-scale elementary flux mode (EFM) computation and uses the OpenMP API to optimally exploit processor architectures with multiple cores., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: FluxModeCalculator (RRID:SCR_016290) Copy   

•   Source: SciCrunch Registry
  

https://lifebit.ai/

Platform for computing management for data analysis on the cloud from the Lifebit company. Allows the computational analyses to be permanently linked to live analyses pipelines.

Proper citation: Lifebit Deploit (RRID:SCR_016428) Copy   

•   Source: SciCrunch Registry
  

http://mib.helsinki.fi/

Software package for advanced image processing, analysis, segmentation and visualization of multi-dimensional (2D-4D) light and electron microscopy datasets.

Proper citation: Microscopy Image Browser (RRID:SCR_016560) Copy   

•   Source: SciCrunch Registry
  

https://www.genome.jp/tools/dinies/

Web server for predicting unknown drug-target interaction networks from various types of biological data in the framework of supervised network inference.

Proper citation: DINIES (RRID:SCR_016505) Copy   

•   Source: SciCrunch Registry
  

https://github.com/WGS-TB/MentaLiST

Software for a MLST (multi-locus sequence typing) caller, based on a k-mer counting algorithm and written in the Julia language. Designed and implemented to handle large typing schemes.

Proper citation: MentaLiST (RRID:SCR_016469) Copy   

•   Source: SciCrunch Registry
  

https://cistem.org/

Software to process cryo-EM images of macromolecular complexes and obtain high-resolution 3D reconstructions from them.

Proper citation: cisTEM (RRID:SCR_016502) Copy   

•   Source: SciCrunch Registry
  

https://pachterlab.github.io/kallisto/about

Software tool for quantifying abundances of transcripts from RNA-Seq data or target sequences using high-throughput sequencing reads.

Proper citation: kallisto (RRID:SCR_016582) Copy   

•   Source: SciCrunch Registry
  

https://github.com/hyattpd/Prodigal

Software tool for protein coding gene prediction for prokaryotic genomes.

Proper citation: Prodigal (RRID:SCR_011936) Copy   

•   Source: SciCrunch Registry
  

http://www.ebi.ac.uk/~zerbino/oases/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software tool as de novo transcriptome assembler designed to produce transcripts from short read sequencing technologies, such as Illumina, SOLiD, or 454 in the absence of any genomic assembly.

Proper citation: Oases (RRID:SCR_011896) Copy   

•   Source: SciCrunch Registry
  

http://tophat.cbcb.umd.edu/fusion_index.html

An algorithm for Discovery of Novel Fusion Transcripts with the ability to align reads across fusion points, which results from the breakage and re-joining of two different chromosomes, or from rearrangements within a chromosome.

Proper citation: TopHat-Fusion (RRID:SCR_011899) Copy   

•   Source: SciCrunch Registry
  

http://cbcb.umd.edu/software/metAMOS

A modular and open source metagenomic assembly and analysis pipeline.

Proper citation: MetAMOS (RRID:SCR_011914) Copy   

•   Source: SciCrunch Registry
  

http://genome.ucsc.edu/cgi-bin/hgBlat?command=start

Software designed to quickly find sequences of 95% and greater similarity of length 25 bases or more.

Proper citation: BLAT (RRID:SCR_011919) Copy   

•   Source: SciCrunch Registry
  

http://www.bios.unc.edu/research/genomic_software/BBSeq/

A Powerful and Flexible Approach to the Analysis of RNA Sequence Count Data.

Proper citation: BBSeq (RRID:SCR_011877) Copy   

•   Source: SciCrunch Registry
  

http://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud/

Software for an iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data with Highly Uneven Sequencing Depth.

Proper citation: IDBA-UD (RRID:SCR_011912) Copy   

•   Source: SciCrunch Registry
  

http://kissplice.prabi.fr/

Software tool that enables analysis of RNA-seq data with or without reference genome. Local transcriptome assembler for SNPs, indels and AS events.

Proper citation: KisSplice (RRID:SCR_011893) Copy   

•   Source: SciCrunch Registry