Curator Dashboard

Software annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms.

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• SciCrunch
• 6 years ago - by Anonymous

Software command line tool for rapidly calculating genome wide sequencing coverage. Measures depth from BAM or CRAM files at either each nucleotide position in genome or for sets of genomic regions. Used for fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing quick coverage calculation for genomes and exomes.

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• SciCrunch
• 6 years ago - by Anonymous

Software tool as pipeline for automatic prediction of genes in eukaryotic genomes based on Softberry gene finding software.

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• SciCrunch
• 6 years ago - by Anonymous

Software fast and lightweight tool for processing sequences in FASTA or FASTQ format.

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• SciCrunch
• 6 years ago - by Anonymous

Software tool as cross platform and ultrafast toolkit for FASTA/Q file manipulation.

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• SciCrunch
• 6 years ago - by Anonymous

Software tool as set of analysis pipelines that processes Chromium sequencing output to align reads and call and phase SNPs, indels, and structural variants by 10x Genomics.

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• SciCrunch
• 6 years ago - by Anonymous

Software tool for computational analysis of gene family evolution. Used for statistical analysis of evolution gene family sizes. Models evolution of gene family sizes over phylogeny.

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• SciCrunch
• 6 years ago - by Anonymous

Software tool as next generation in LC-MS proteomics data analysis software by Nonlinear Dynamics.

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• RRID-Legacy
• 6 years ago - by Anonymous

Software package to identify genomic insertions or deletions, so called indels, in heterozygous sequencing data where both alleles carry mutations. Used to analyze heterozygous indels.

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• RRID-Legacy
• 6 years ago - by Anonymous

Software drug discovery platform to integrate purchasable chemical space with molecular modeling tools. Chemical marketplace for drug discovery with services based around small molecule compound sourcing. Integrated molecular modeling tools, compound database, IT infrastructure and compound procurement service with web interface. Virtual screens can be run to identify new hits and modeling applications can be used to improve their affinity and other properties.

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• SciCrunch
• 6 years ago - by Anonymous

The Smart-seq2 Single Nucleus Multi-Sample (Multi-snSS2) pipeline was developed in collaboration with the BRAIN Initiative Cell Census Network (BICCN) to process single-nucleus RNAseq (snRNAseq) data generated by Smart-seq2 assays.

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• RRID-Legacy
• 6 years ago - by Anonymous

Pipeline developed in collaboration with Bing Ren lab and supports processing of BICCN single-cell/nucleus ATAC-seq datasets. Pipeline uses python module SnapTools to align and process paired reads in form of FASTQ files. Produces hdf5-structured Snap file that includes cell-by-bin count matrix. Final outputs also include GA4GH compliant aligned BAM and QC metrics.

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• RRID-Legacy
• 6 years ago - by Anonymous

Software R package to identify active pairs of ligand receptors from single cells in order to study,among others, tumor host interactions. Contains set of signatures to classify cells from tumor microenvironment.

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• SciCrunch
• 6 years ago - submitted by Michele Ceccarelli

Processor that automatically washes tissue sample which needs to be usable in downstream processes. Designed for routine and research histopathology of up to 300 cassettes.

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• RRID-Legacy
• 6 years ago - submitted by Gabrielle Pine

Open source software tool for file based localization of numerical perturbations in data analysis pipelines. Identifies components in pipeline, at resolution level of system process, that produce different results in different execution conditions.

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• RRID-Legacy
• 6 years ago - submitted by Ali Salari

Group of academic institutions committed to studying diabetic foot conditions, such as foot ulcers and wound healing, to develop predictive biomarkers which can be later used to create better treatment plans and improve health and quality of life for people living with diabetes.

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• dkNET
• 6 years ago - submitted by Ko-Wei Lin

Project to bridge gap between in vitro human islet studies and clinical studies in human subjects. Used to integrate cellular and medical research data, collected by partners, with computational modelling to identify pathophysiological mechanisms and markers of spectrum of biological and cellular processes involved in pancreatic beta cell failure leading to impaired glucose tolerance and T2D.

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• dkNET
• 6 years ago - submitted by Ko-Wei Lin

Webserver to process, analyse and visualize Oxford Nanopore Technologies (ONT) data and similar long-reads technologies. Collection of best practice and popular ONT-oriented tools are integrated in this custom Galaxy instance.

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• SciCrunch
• 6 years ago - submitted by Willem de Koning

Course provides training for reproducible analyses of Adolescent Brain Cognitive Development Study data. Designed to provide comprehensive background to ABCD study while delivering hands on instruction on reproducible ReproNim workflows and outcomes.

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• NIF
• 6 years ago - by Anonymous

Database of protein abundance averages across all three domains of life. Protein abundance database, which contains whole genome protein abundance information across organisms and tissues. Publicly available experimental data are imported and mapped onto common name space and, in case of tandem mass spectrometry data, re-processed using in-house standardized spectral counting pipeline. All datasets in are scored and ranked by importing protein network information. Orthology relations at various hierarchy levels are pre-computed for each protein.

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• RRID-Legacy
• 6 years ago - submitted by Anita Bandrowski