Tools   Select Another Resource Report Type

https://github.com/TransDecoder/TransDecoder

Software tool to identify candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to genome using Tophat and Cufflinks.Starts from FASTA or GFF file. Can scan and retain open reading frames (ORFs) for homology to known proteins by using BlastP or Pfam search and incorporate results into obtained selection. Predictions can then be visualized by using genome browser such as IGV.

Proper citation: TransDecoder (RRID:SCR_017647) Copy   

•   Source: SciCrunch Registry

http://spark.apache.org/

Software tool as a unified analytics engine for large scale data processing. An open source distributed general purpose cluster computing framework.

Proper citation: Apache Spark (RRID:SCR_016557) Copy   

•   Source: SciCrunch Registry

https://github.com/kendomaniac/docker4seq

Software R package to execute next generation sequencing computing applications, e.g. reads mapping and counting, wrapped in docker containers.

Proper citation: docker4seq (RRID:SCR_017006) Copy   

•   Source: SciCrunch Registry

https://github.com/shendurelab/LACHESIS

Software tool for chromosome scale scaffolding of de novo genome assemblies based on chromatin interactions.Method exploits signal of genomic proximity in Hi-C datasets for ultra long range scaffolding of de novo genome assemblies.

Proper citation: LACHESIS (RRID:SCR_017644) Copy   

•   Source: SciCrunch Registry

https://github.com/OpenGene/AfterQC

Software that performs automatic filtering, trimming, error removing, and quality control for fastq data.

Proper citation: AfterQC (RRID:SCR_016390) Copy   

•   Source: SciCrunch Registry

https://github.com/facebook/prophet

Open source software package for producing forecasts for time series data that has multiple seasonality with linear or non linear growth. Implemented in R or Phyton.

Proper citation: Prophet (RRID:SCR_017083) Copy   

•   Source: SciCrunch Registry

http://regent.qc.ca/assets/winrhizo_software.html

Software toolbox for image analysis by Regent Instruments Inc. Used for root measurement in different forms like morphology, topology, architecture and color analyses. Automatically or interactively analyses washed roots.

Proper citation: WinRHIZO (RRID:SCR_017120) Copy   

•   Source: SciCrunch Registry

http://www.ccp4.ac.uk/html/aimless.html

Data processing software for x-ray diffraction data. AIMLESS scales together multiple observations of reflections, and merges multiple observations into an average intensity.

Proper citation: AIMLESS (RRID:SCR_015747) Copy   

•   Source: SciCrunch Registry

https://www.globalphasing.com/autoproc/

Data processing software for X-ray diffraction data. autoPROC is a set of tools and programs to automate steps involved in data processing, such as image analysis, integration, indexing, and determination.

Proper citation: autoPROC (RRID:SCR_015748) Copy   

•   Source: SciCrunch Registry

https://github.com/TeamMacLean/atacr

Software that analyzes count data from RNA-capture-seq and ATAC-capture-seq experiments. Using BioConductor RangedSummarizedExperiment objects, atacr implements a set of helper functions and quality control plots specific to the analysis of counts of reads in windows across genomes.

Proper citation: atacr (RRID:SCR_016286) Copy   

•   Source: SciCrunch Registry

http://www.studylog.com

Commerciall organization to develop study protocols collaboratively to run and manage animal research studies for academic, government, biotech and pharmaceutical labs. Provides services, including product installation and configuration, user training, customization services and ongoing support.

Proper citation: Studylog (RRID:SCR_016682) Copy   

•   Source: SciCrunch Registry

https://github.com/kstreet13/slingshot

Software R package for identifying and characterizing continuous developmental trajectories in single cell data. Cell lineage and pseudotime inference for single-cell transcriptomics.

Proper citation: Slingshot (RRID:SCR_017012) Copy   

•   Source: SciCrunch Registry

Ratings or validation data are available for this resource

https://github.com/BodenmillerGroup/imctools

Software Python package that implements preprocessing pipeline for imaging mass cytometry data. Can convert IMC raw files to tiff files that are used as inputs into CellProfiller, Ilastik, Fiji etc.

Proper citation: imctools (RRID:SCR_017132) Copy   

•   Source: SciCrunch Registry

https://bitbucket.org/mroachawri/purge_haplotigs/src

Pipeline for reassigning primary contigs that should be labelled as haplotigs. Used for third generation sequencing based assemblies to automate reassignment of allelic contigs, and to assist in manual curation of genome assemblies.

Proper citation: Purge_haplotigs (RRID:SCR_017616) Copy   

•   Source: SciCrunch Registry

https://www.synapse.org/#!Synapse:syn4921369/wiki/235539

Portal of PsychENCODE Consortium to study role of rare genetic variants involved in several psychiatric disorders. Database of regulatory elements, epigenetic modifications, RNA and protein in brain.

Proper citation: PsychENCODE Knowledge Portal (RRID:SCR_017500) Copy   

•   Source: SciCrunch Registry

https://github.com/colinvaz/nmf-toolbox

Software toolbox for performing Non-negative Matrix Factorization (NMF) and several variants. Used to factorize one non negative matrix into two non negative factors, that is basis matrix and coefficient matrix. Applied in bioinformatics as data mining approach.

Proper citation: NMF Toolbox (RRID:SCR_017069) Copy   

•   Source: SciCrunch Registry

https://www.sanger.ac.uk/science/tools/reapr

Software tool to identify errors in genome assemblies without need for reference sequence. Can be used in any stage of assembly pipeline to automatically break incorrect scaffolds and flag other errors in assembly for manual inspection. Reports mis-assemblies and other warnings, and produces new broken assembly based on error calls.

Proper citation: Recognition of Errors in Assemblies using Paired Reads (RRID:SCR_017625) Copy   

•   Source: SciCrunch Registry

https://drugs.ncats.io/

Portal of NCATS (the National Center for Advancing Translational Sciences) for drug development information including:US approved drugs, marketed drugs, investigational drugs. Provides manually curated data supplied by the FDA and private companies. Provides drugs marketing and regulatory status, drug ingredient definitions, biological activity and clinical use.

Proper citation: Inxight (RRID:SCR_016490) Copy   

•   Source: SciCrunch Registry

http://www.vilber.de/en/products/analysis-software/capt-software/

Software for molecular weight, quantification of bands, colony counting and distance calculation in Vilber Lourmat gel documentation imaging systems. Used in molecular biology laboratories.

Proper citation: CAPT (RRID:SCR_016305) Copy   

•   Source: SciCrunch Registry

https://github.com/AlexsLemonade/refinebio

Software tool to uniformly process and normalize large amounts of data. Harmonizes petabytes of publicly available biological data into ready-to-use datasets for cancer researchers and AI/ML scientists.

Proper citation: refine.bio (RRID:SCR_017471) Copy   

•   Source: SciCrunch Registry