Curator Dashboard

Software DICOM library which provides user-friendly C++11 and Python API for different parts of the DICOM standard.

• Resource
• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Online predictor of NOn-Regular Secondary Structure for disordered regions in protein. Used to predict long regions with no regular secondary structure. Upon user submission of protein sequence, NORSp will analyse the protein about its secondary structure, and presence of transmembrane helices and coiled-coil then return e-mail to user about the presence and position of disordered regions.

• Resource
• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool as alignment program for protein sequence-to-sequence alignments based on the standard Needleman-Wunsch dynamic programming algorithm.

• Resource
• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool as tree drawing program to draw any phylogenetic tree expressed in Newick phylogenetic tree format (e.g., the format used by the PHYLIP package).Used for rooting the unrooted trees obtained from parsimony, distance or maximum likelihood tree-building methods.

• Resource
• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software provides access to NCBI's suite of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from Unix terminal window. Search terms are entered as command-line arguments. Individual operations are connected with Unix pipes to construct multi-step queries. Selected records can then be retrieved in variety of formats.

• Resource
• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software workflow manager that enables development of portable and reproducible workflows.Supports deploying workflows on variety of execution platforms including local, HPC schedulers, AWS Batch, Google Cloud Life Sciences, and Kubernetes. Provides support to manage workflow dependencies through built-in support for Conda, Spack, Docker, Podman, Singularity, Modules, and more.

• Resource
• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool for automated structrual variation detection from long-read sequencing using state-of-the-art tools. NextSV3 uses Minimap2 to do read mapping and uses two state-of-the-art SV callers (Sniffles and cuteSV) to do SV calling.

• Resource
• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software alignment program that can align pairs of sequences using logarithmic and affine gap penalties.

• Resource
• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software language-theory based homology detection tool across multiple large genomes.

• Resource
• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software library of sequence alignment algorithms implemented in Java.

• Resource
• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool as partner script to the popular ncbi-genome-download script. Allows to download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API.

• Resource
• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Web-compatible database search or multiple alignment viewer, Software tool as command line utility that extracts and reformats the results of a sequence database search or a multiple alignment, optionally adding HTML markup for web page layout. It can also be used as a filter to extract and convert searches or alignments to common formats.

• Resource
• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software package as plotting tool for long read sequencing data and alignments.

• Resource
• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software package that can be used to identify structural genomic variations in long-read sequencing data, such as data produced by Oxford Nanopore Technologies� MinION, GridION or PromethION instruments, or Pacific Biosciences RSII or Sequel sequencers.

• Resource
• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool for structural alignment of multiple protein structures. Used to produce sequence alignment. Reports multiple sequence alignment and corresponding superposition of structures.

• Resource
• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software package to remove reads mapping to the lambda phage genome from a fastq file.

• Resource
• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software basecaller for Oxford Nanopore Technologies sequencing data. Oxford Nanopore Basecaller.

• Resource
• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tools to perform various types of diffusion MRI analyses, from various forms of tractography through to next-generation group-level analyses.

• Resource
• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Open source multi platform molecular visualization program.

• Resource
• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool for single locus species delimitation. Implements fast method to compute the ML delimitation from inferred phylogenetic tree of the samples.Used to handle very large biodiversity datasets.

• Resource
• SciCrunch
• 3 years ago - submitted by Edyta Vieth