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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
Software toolkit for gray scale medical image analysis. Provides combination of command line tools, plug-ins, and libraries that make it possible to run image processing tasks interactively in command shell and prototype algorithms as shell scripts. MIA is build around a plug-in structure that makes it easy to add functionality without compromising the original code base, and it makes use of wide variety of external libraries that provide additional functionality.
Proper citation: MIA (RRID:SCR_024081) Copy
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
http://www.nematodes.org/bioinformatics/trace2dbEST/
Software tool to process raw sequenceing chromatograph trace files from EST projects into quality checked sequences, ready for submission to dbEST.
Proper citation: trace2dbEST (RRID:SCR_024386) Copy
https://github.com/sina-cb/Tn-seqExplorer
Software package written in Java for analysis of high-throughput sequencing data of transposon mutant libraries.Reads the alignment and the gene annotation, and provides the user with set of tools to investigate data and identify possibly essential or advantageous genes as those that contain significantly low counts of transposon insertions.
Proper citation: Tn-seq explorer (RRID:SCR_024387) Copy
http://saclab.tamu.edu/essentiality/transit/
Software tool for Himar1 TnSeq analysis.Provides graphical interface to three different statistical methods for analyzing TnSeq data. Used for identifying essential genes in individual datasets as well as comparative analysis between conditions.
Proper citation: TRANSIT (RRID:SCR_024389) Copy
Software tool to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood. Allows analysis of large data sets and automatically assigns estimations of support to each internal branch. Computes pairwise maximum likelihood distances as well as branch lengths for user specified trees.Conducts statistical tests on the data set.
Proper citation: TREE-PUZZLE (RRID:SCR_024382) Copy
https://github.com/bartongroup/yanosim
Software tool as read simulator for nanopore DRS datasets.
Proper citation: Yanosim (RRID:SCR_024363) Copy
https://www.bioinformatics.org/~tryphon/populations/
Population genetic software for individuals or populations distances based on allelic frequencies, phylogenetic trees, file conversions.
Proper citation: Populations (RRID:SCR_024175) Copy
https://github.com/khowe/quicktree/
Software application as implementation of Neighbor-Joining algorithm, capable of reconstructing phylogenies from huge alignments.
Proper citation: quicktree (RRID:SCR_024205) Copy
https://github.com/a-slide/pycoQC
Software application to compute metrics and generate interactive QC plots for Oxford Nanopore technologies sequencing data.
Proper citation: pycoqc (RRID:SCR_024185) Copy
https://docs.airr-community.org/en/latest/packages/airr-python/overview.html
Software airr reference library provides basic functions and classes for interacting with AIRR Community Data Representation Standards, including tools for read, write and validation.
Proper citation: python-airr (RRID:SCR_024187) Copy
https://bioconductor.org/packages/release/bioc/html/annotate.html
Software R package for using R enviroments for annotation.
Proper citation: annotate (RRID:SCR_024221) Copy
https://sourceforge.net/projects/tab2mage/
Software package written and supported by the ArrayExpress curation team, which aims to ease the process of submitting large microarray experiment datasets.Tab2MAGE uses flexible spreadsheet format for MIAME annotation of microarray experiments.Spreadsheets may be submitted directly to ArrayExpress, or used to generate MAGE-ML for data exchange.
Proper citation: Tab2MAGE (RRID:SCR_024101) Copy
http://colibread.inria.fr/software/mapsembler2/
Targeted assembly software. It takes as input any number of NGS raw read sets and starter set of input sequences.May be used to Validate assembled sequence, Check if known enzyme is present in metagenomic NGS read set, Enrich unmappable reads by extending them, Check what happens at the extremities of a contig, Check the presence / absence and quantify RNA seq splicing events, Check presence/absence of SNPs or structural variants.
Proper citation: Mapsembler2 (RRID:SCR_024102) Copy
https://bioconductor.org/packages/release/bioc/html/affyio.html
Software R package as routines for parsing Affymetrix data files based upon file format information. Primary focus is on accessing CEL and CDF file formats.
Proper citation: affyio (RRID:SCR_024223) Copy
https://github.com/gerddie/maxflow
Software library that implements the maxflow-mincut algorithm.Used for computing mincut/maxflow in a graph.
Proper citation: MAXFLOW (RRID:SCR_024103) Copy
https://bioconductor.org/packages/release/bioc/html/altcdfenvs.html
Software R package contains convenience data structures and functions to handle cdfenvs.
Proper citation: altcdfenvs (RRID:SCR_024225) Copy
https://github.com/aschafu/PSSH2
Software tools for creating the sequence-to-structure alignment database PSSH2.
Proper citation: pssh2 (RRID:SCR_024181) Copy
https://pyepl.sourceforge.net/
Software library for coding psychology experiments in Python.Supports presentation of both visual and auditory stimuli, and supports both manual and sound input as responses.
Proper citation: pyepl (RRID:SCR_024182) Copy
https://github.com/PacificBiosciences/pbcopper
Software library provides suite of data structures, algorithms, and utilities for PacBio C++ applications.
Proper citation: pbcopper (RRID:SCR_024152) Copy
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