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http://tools.thermofisher.com/content/sfs/manuals/nd-1000-v3.8-users-manual-8%205x11.pdf
Spectrophotometer for measurement and analysis of 1 ul samples with high accuracy and reproducibility. Full spectrum from 220nm to 750nm spectrophotometer utilizes patented sample retention technology that employs surface tension alone to hold sample in place. No need for cuvettes. Has capability to measure highly concentrated samples without dilution.
Proper citation: Thermo Fisher: Nanodrop 1000 Spectrophotometer (RRID:SCR_016517) Copy
https://www.mrc-lmb.cam.ac.uk/kzhang/Gctf/
Software tool as a Graphics Processing Units (GPU) accelerated computer program for real-time contrast transfer function (CTF) determination and correction. Used for a near-atomic resolution cryo electron microscopy (cryoEM) reconstruction to maximize the cross-correlation of a simulated CTF with the logarithmic amplitude spectra (LAS) of observed micrographs after background subtraction., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: GCTF (RRID:SCR_016500) Copy
Database and information retrieval, analysis, and visualization system for microbial resources to help culture collections to manage, disseminate and share the information related to their holdings. Provides an interface for the scientific and industrial communities to access the microbial resource information.
Proper citation: Global Catalogue of Microorganisms (RRID:SCR_016460) Copy
https://github.com/tomazc/iCount
Software Python package for protein-RNA interaction analysis. Used for analysis of protein-RNA interactions with iCLIP sequencing data and RNA maps.
Proper citation: iCount (RRID:SCR_016712) Copy
http://www.fon.hum.uva.nl/praat/
Software tool for phonetics research to analyse, synthesize, and manipulate speech.
Proper citation: Praat (RRID:SCR_016564) Copy
Software toolbox for MATLAB for the descriptive and inferential statistical analysis of directional data.
Proper citation: circular statistics (RRID:SCR_016651) Copy
https://doi.org/10.1016/j.neuroimage.2018.07.046
Software package for simulation framework and codes for estimating nonparametric Granger causality. Used to study brain functions.
Proper citation: nonparametricGGC_toolbox (RRID:SCR_016539) Copy
https://gitlab.com/danio-code/public/dcc
Software tool as an annotation structure and user-hosted platform for sequencing experiment data, suitable for lab-internal documentation, collaborations and large-scale annotation efforts.
Proper citation: DCC (RRID:SCR_016544) Copy
https://github.com/vaklip/transfer_learning_ccnn
Software program to implement transfer learning for a connectome convolutional neural network trained to classify functional connectomes using Tensorflow.
Proper citation: transfer_ learning_ ccnn (RRID:SCR_016590) Copy
Software as graphical and interactive tool dedicated to 1D spectra processing for NMR-based metabolomics.
Proper citation: NMRProcFlow (RRID:SCR_016592) Copy
https://www.ncbi.nlm.nih.gov/projects/mutagene/
Software tool to explore and analyze mutagenic factors leading to tumors to decipher cancer genetic heterogeneity.
Proper citation: MutaGene (RRID:SCR_016574) Copy
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
https://github.com/ToolsVanBox/smMIPfil
Software tool for single molecule Molecular Inversion Probes data analysis. This is a stand-alone perl script. Except that this is dependent on the samtools, no installation required.
Proper citation: smMIPfil (RRID:SCR_016892) Copy
https://github.com/Crick-CancerGenomics/ascat
Software R package to infer tumor purity, ploidy and allele-specific copy number profiles. It is platform and species independent, and works for both Illumina and Affymetrix SNP arrays, as well as for massively parallel sequencing data.
Proper citation: ascat (RRID:SCR_016868) Copy
https://github.com/aroth85/pyclone
Software tool to infer the prevalence of point mutations in heterogeneous cancer samples. Probabilistic model for inferring clonal population structure from deep NGS sequencing.
Proper citation: Pyclone (RRID:SCR_016873) Copy
https://github.com/dpeerlab/phenograph
Software tool as clustering method designed for high dimensional single cell data. Algorithmically defines phenotypes in high dimensional single cell data. Used for large scale analysis of single cell heterogeneity.
Proper citation: Phenograph (RRID:SCR_016919) Copy
http://grigoriefflab.janelia.org/ctffind4
Software tool for finding CTFs of electron micrographs. Program used for the estimation of objective lens defocus parameters from transmission electron micrographs. The program CTFFIND3 is an updated version of the program CTFFIND2. For micrographs collected on photographic film and scanned in use CTFFIND 3. For images from CCDs or direct detectors use CTFFIND 4.
Proper citation: CTFFIND (RRID:SCR_016732) Copy
https://github.com/kendomaniac/rCASC
Software package for reproducible classification analysis of single cell sequencing data.
Proper citation: rCASC (RRID:SCR_017005) Copy
https://github.com/Rinoahu/SwiftOrtho
Software tool for orthology analysis to identify orthologs, paralogs and co orthologs for genomes. Used to perform homology classification across genomes of different species in large genomic datasets.
Proper citation: SwiftOrtho (RRID:SCR_017122) Copy
https://github.com/cancerit/cgpBattenberg
Software tool as installation helper, perl wrapper and R program Battenberg which detects subclonality and copy number in matched NGS data.
Proper citation: cgpBattenberg (RRID:SCR_017092) Copy
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