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http://harvester.fzk.de/harvester/

Harvester is a Web-based tool that bulk-collects bioinformatic data on human proteins from various databases and prediction servers. It is a meta search engine for gene and protein information. It searches 16 major databases and prediction servers and combines the results on pregenerated HTML pages. In this way Harvester can provide comprehensive gene-protein information from different servers in a convenient and fast manner. As full text meta search engine, similar to Google trade mark, Harvester allows screening of the whole genome proteome for current protein functions and predictions in a few seconds. With Harvester it is now possible to compare and check the quality of different database entries and prediction algorithms on a single page. Sponsors: This work has been supported by the BMBF with grants 01GR0101 and 01KW0013.

Proper citation: Bioinformatic Harvester IV (beta) at Karlsruhe Institute of Technology (RRID:SCR_008017) Copy   

•   Source: SciCrunch Registry

http://darcsite.genzentrum.lmu.de/darc/

A database for aligned ribosomal complexes that provides a resource for directly comparing the structures. A collection of files deposited in the RCSB protein data bank and the Electron Microscopy Data Bank have been aligned so as to make direct comparison of the structures possible. An easy-to-use, searchable interface allows users to access and download >130 cryo-EM maps and >300 atomic models in the format of brix and pdb files, respectively. The aligned coordinate system substantially simplifies direct visualization of conformational changes in the ribosome, such as subunit rotation and head-swiveling, as well as direct comparison of bound ligands, such as antibiotics or translation factors.

Proper citation: DARC - Database for Aligned Ribosomal Complexes (RRID:SCR_006932) Copy   

•   Source: SciCrunch Registry

http://www.plexdb.org/index.php

PLEXdb (Plant Expression Database) is a unified gene expression resource for plants and plant pathogens. PLEXdb is a genotype to phenotype, hypothesis building information warehouse, leveraging highly parallel expression data with seamless portals to related genetic, physical, and pathway data. The integrated tools of PLEXdb allow investigators to use commonalities in plant biology for a comparative approach to functional genomics through use of large-scale expression profiling data sets.

Proper citation: PLEXdb - Plant Expression Database (RRID:SCR_006963) Copy   

•   Source: SciCrunch Registry

http://gwyddion.net/

Modular program for SPM (scanning probe microscopy) data visualization and analysis. Primarily it is intended for the analysis of height fields obtained by scanning probe microscopy techniques (AFM, MFM, STM, SNOM/NSOM) and it supports a lot of SPM data formats. However, it can be used for general height field and (greyscale) image processing, for instance for the analysis of profilometry data or thickness maps from imaging spectrophotometry.

Proper citation: Gwyddion (RRID:SCR_015583) Copy   

•   Source: SciCrunch Registry

http://pasapipeline.github.io/

Gene structure annotation and analysis tool that uses spliced alignments of expressed transcript sequences to automatically model gene structures. It also incorporates gene structures based on transcript alignments into existing gene structure annotations. It is one component of a larger eukayotic annotation pipeline implemented at the Broad Institute.

Proper citation: PASA (RRID:SCR_014656) Copy   

•   Source: SciCrunch Registry

https://github.com/nbcrrolls/workflows/tree/master/Production/AmberGPUMDSimulation

A workflow for running molecular dynamics simulations. It can be used for all-atom molecular dynamic simulations, which involve five steps of minimization, one step of heating, three steps of equilibration, and one or more instances of production. The input is a set of directories that include the MD simulation input scripts, system topology and coordinate files. Output files are list of plots, simulation trajectories, intermediate files, restart files, and the like.

Proper citation: Molecular Dynamics Workflow (BioKepler) (RRID:SCR_014389) Copy   

•   Source: SciCrunch Registry

https://atgu.mgh.harvard.edu/plinkseq/

An open-source C/C++ library for working with human genetic variation data. The specific focus is to provide a platform for analytic tool development for variation data from large-scale resequencing projects, particularly whole-exome and whole-genome studies. However, the library could in principle be applied to other types of genetic studies, including whole-genome association studies of common SNPs. (entry from Genetic Analysis Software)

Proper citation: PLINK/SEQ (RRID:SCR_013193) Copy   

•   Source: SciCrunch Registry

https://github.com/csb-toolbox/CSB

Software package as an application framework and a Python class library. It is designed for reading, storing and analyzing biomolecular structures in a variety of formats with rich support for statistical analyses.

Proper citation: Computational Structural Biology Toolbox (RRID:SCR_016065) Copy   

•   Source: SciCrunch Registry

https://github.com/nservant/HiC-Pro

Software tool as optimized and flexible pipeline for Hi-C data processing. Used to process Hi-C data, from raw fastq files, paired end Illumina data, to normalized contact maps.

Proper citation: HiC-Pro (RRID:SCR_017643) Copy   

•   Source: SciCrunch Registry

https://github.com/davidemms/OrthoFinder

Software Python application for comparative genomics analysis. Finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of gene duplcation events in those gene trees, infers rooted species tree for species being analysed and maps gene duplication events from gene trees to branches in species tree, improves orthogroup inference accuracy. Runs set of protein sequence files, one per species, in FASTA format.

Proper citation: OrthoFinder (RRID:SCR_017118) Copy   

•   Source: SciCrunch Registry

https://github.com/mikelove/tximport

Software R package for importing pseudoaligned reads into R for use with downstream differential expression analysis. Used for import and summarize transcript level estimates for transcript and gene level analysis.

Proper citation: tximport (RRID:SCR_016752) Copy   

•   Source: SciCrunch Registry

https://nephele.niaid.nih.gov

Cloud based platform for simplified, standardized and reproducible microbiome data analysis. Allows users to process microbiome datasets through pipelines of existing software tools.

Proper citation: Nephele (RRID:SCR_016595) Copy   

•   Source: SciCrunch Registry

https://github.com/theislab/scanpy

Software Python tool for large scale single cell gene expression data analysis. Integrates analysis possibilities of established R-based frameworks, provides pre processing, visualization, graph-drawing and diffusion maps, clustering, identification of marker genes for clusters via differential expression tests and pseudo temporal ordering via diffusion pseudo time.

Proper citation: scanpy (RRID:SCR_018139) Copy   

•   Source: SciCrunch Registry

https://github.com/broadinstitute/Drop-seq

Software Java tools for analyzing Drop-seq data. Used to analyze gene expression from thousands of individual cells simultaneously. Analyzes mRNA transcripts while remembering origin cell transcript.

Proper citation: Drop-seq tools (RRID:SCR_018142) Copy   

•   Source: SciCrunch Registry

https://github.com/lkmklsmn/DrivAER

Software tool as method for identification of driving transcriptional programs based on AutoEncoder derived Relevance scores. Infers relevance scores for transcriptional programs with respect to specified outcomes of interest in single-cell RNA sequencing data, such as psuedotemporal ordering or disease status.Used for manifold interpretation in scRNA-seq data.

Proper citation: DrivAER (RRID:SCR_019076) Copy   

•   Source: SciCrunch Registry

https://github.com/wilkinsonlab/epigenomics_pipeline

Software tool as epigenomics analysis pipeline for analysis of ChIP-Seq and RNA-Seq data using Docker images containing Galaxy and Jupyter.

Proper citation: Epigenomics Workflow on Galaxy and Jupyter (RRID:SCR_017544) Copy   

•   Source: SciCrunch Registry

http://www.imgt.org/HighV-QUEST/home.action

Next generation B and T cell sequence alignment and characterization online surface by IMGT. Web portal for immunoglobulin (IG) or antibody and T cell receptor (TR) analysis from NGS high throughput and deep sequencing.

Proper citation: IMGT HighV-QUEST (RRID:SCR_018196) Copy   

•   Source: SciCrunch Registry

https://pm4ngs.readthedocs.io/

Software tool to generate standard organizational structure for Next Generation Sequencing data analysis. Includes directory structure for project, several Jupyter notebooks for data management and CWL workflows for pipeline execution.

Proper citation: PM4NGS (RRID:SCR_019164) Copy   

•   Source: SciCrunch Registry

https://github.com/ANGSD/ngsRelate

Software tool for estimating pairwise relatedness from next-generation sequencing data.

Proper citation: ngsRelate (RRID:SCR_016588) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/ComplexHeatmap.html

Software package to arrange multiple heatmaps and support various annotation graphics. Used to visualize associations between different sources of data sets and to reveal potential patterns.

Proper citation: ComplexHeatmap (RRID:SCR_017270) Copy   

•   Source: SciCrunch Registry