Tools   Select Another Resource Report Type

https://awi.cuhk.edu.cn/KinasePhos/download.html

Software tool for redesign and expansion of prediction on kinase specific phosphorylation sites. Machine learning based kinase specific phosphorylation site prediction tool.

Proper citation: KinasePhos 3.0 (RRID:SCR_023595) Copy   

•   Source: SciCrunch Registry

https://rth.dk/resources/risearch/

Software tool for prediction of RNA–RNA, RNA–DNA, and DNA–DNA interactions. Both RIsearch1 and RIsearch2 enable quick localisation of potential near complementary interactions between given query and target sequences. RIsearch1 performs computation with whole sequences. RIsearch2 focuses on perfect complementary seed regions and extends them on both ends. User defined seed and extension constraints makes RIsearch2 applicable to all kinds of interaction predictions (e.g., siRNA and Cas9–gRNA off-target predictions).

Proper citation: RIsearch (RRID:SCR_023503) Copy   

•   Source: SciCrunch Registry

https://rostlab.org/owiki/index.php/PROFisis

Software tool that identifies interacting residues from sequence alone. Developed using transient protein�protein interfaces from complexes of experimentally known 3D structures.

Proper citation: PROFisis (RRID:SCR_024179) Copy   

•   Source: SciCrunch Registry

http://contra.stanford.edu/contrafold/

Software novel secondary structure prediction method based on conditional log-linear models, a flexible class of probabilistic models which generalize upon SCFGs by using discriminative training and feature-rich scoring. Used for sequence prediction.

Proper citation: CONTRAfold (RRID:SCR_023994) Copy   

•   Source: SciCrunch Registry

https://github.com/bioinfo-center-pasteur-fr/toppred

Software tool for membrane protein structure prediction.Transmembrane topology prediction.Used for predicting topology of bacterial inner membrane proteins.

Proper citation: toppred (RRID:SCR_024385) Copy   

•   Source: SciCrunch Registry

https://github.com/paulgeeleher/pRRophetic

Software R package for prediction of clinical chemotherapeutic response from tumor gene expression levels. Used to predict phenotypes from gene expression microarray data, gene expression microarray data,

Proper citation: pRRophetic (RRID:SCR_024417) Copy   

•   Source: SciCrunch Registry

https://rostlab.org/owiki/index.php/Metastudent

Software tool to predict gene ontology terms for protein sequences through homology.

Proper citation: Metastudent (RRID:SCR_024110) Copy   

•   Source: SciCrunch Registry

https://github.com/bartongroup/yanosim

Software tool as read simulator for nanopore DRS datasets.

Proper citation: Yanosim (RRID:SCR_024363) Copy   

•   Source: SciCrunch Registry

http://www.ctsim.org

Software tool to simulate process of transmitting X-rays through phantom objects. Reconstructs original phantom image from projections. Has wide array of image analysis and image processing functions.

Proper citation: CTSim (RRID:SCR_024004) Copy   

•   Source: SciCrunch Registry

https://community.brain-map.org/t/allen-human-reference-atlas-3d-2020-new/405

Parcellation of adult human brain in 3D, labeling every voxel with brain structure spanning 141 structures. These parcellations were drawn and adapted from prior 2D version of adult human brain atlas.

Proper citation: Allen Human Reference Atlas, 3D, 2020 (RRID:SCR_017764) Copy   

•   Source: SciCrunch Registry

http://tools.thermofisher.com/content/sfs/manuals/cms_040970.pdf

Automated PCR instrument for automated amplification of nucleic acids with Polymerase Chain Reaction. It has reaction volumes of up to 50 uL and sample temperature range of 4 to 99.9 C.

Proper citation: Thermo Fisher: Applied Biosystems: GeneAmp 9700 PCR Thermocycler System (RRID:SCR_018436) Copy   

•   Source: SciCrunch Registry

https://github.com/ttrogers/DecodingDynamic

Data, code, and notebooks for replicating analyses reported in Rogers et al., Evidence for deep, distributed and dynamic semantic code in human ventral anterior temporal cortex.

Proper citation: DecodingDynamic (RRID:SCR_021099) Copy   

•   Source: SciCrunch Registry

https://kimlab.io/brain-map/atlas/

Labels provide resource to isolate and identify mouse brain anatomical structures. Cell type specific transgenic mice and an MRI atlas were used to adjust and further segment the labels. Highly segmented anatomical labels in the adult mouse brain common coordinate framework.

Proper citation: Enhanced and Unified Anatomical Labeling for Common Mouse Brain Atlas (RRID:SCR_022816) Copy   

•   Source: SciCrunch Registry

https://drive.google.com/drive/folders/1K5oiXPcZDPT40irrZ_G2hZ86uNGA7CYZ?usp=sharing

Reference atlas for mice. Contains both average and annotation templates.

Proper citation: fMOST Atlas (RRID:SCR_022868) Copy   

•   Source: SciCrunch Registry

https://metacpan.org/dist/Bio-EUtilities

Software package which interacts with and retrieves data from NCBI's eUtils. This distribution encompasses low-level API for interacting with (and storing) information from NCBI's eUtils interface. See Bio::DB::EUtilities for the query API to retrieve data from NCBI, and Bio::Tools::EUtilities for the general class storage system. Note this may change to utilize the XML schema for each class at some point, though we will attempt to retain current functionality for backward compatibility unless this becomes problematic.

Proper citation: Bio-EUtilities (RRID:SCR_024064) Copy   

•   Source: SciCrunch Registry

https://metacpan.org/dist/Bio-Tools-Run-Alignment-Clustalw

Software package for performing multiple sequence alignment from set of unaligned sequences and/or sub-alignments by means of the clustalw program.

Proper citation: Bio-Tools-Run-Alignment-Clustalw (RRID:SCR_024067) Copy   

•   Source: SciCrunch Registry

https://metacpan.org/dist/Bio-Tools-Phylo-PAML

Software package used to parse output from the PAML programs codeml, baseml, basemlg, codemlsites and yn00. You can use the Bio-Tools-Run-Phylo-PAML modules to actually run some of the PAML programs, but this module is only useful to parse the output.

Proper citation: Bio-Tools-Phylo-PAML (RRID:SCR_024069) Copy   

•   Source: SciCrunch Registry

https://metacpan.org/dist/Bio-Graphics

Software package to generate GD images of Bio::Seq objects.

Proper citation: Bio-Graphics (RRID:SCR_024061) Copy   

•   Source: SciCrunch Registry

https://github.com/genouest/biomaj-cli

Software package to use BioMAJ providing biomaj-cli.

Proper citation: CLI for BioMAJ (RRID:SCR_023980) Copy   

•   Source: SciCrunch Registry

https://github.com/dutilh/CAT

Software pipeline for taxonomic classification of contigs and metagenome-assembled genomes. Contig Annotation Tool and Bin Annotation Tool for the taxonomic classification of long DNA sequences and metagenome assembled genomes of both known and unknown microorganisms, as generated by contemporary metagenomics studies.

Proper citation: CAT and BAT (RRID:SCR_023988) Copy   

•   Source: SciCrunch Registry