Curator Dashboard

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

The generatation of GPR120-IRES-EGFP knockin mouse Insufficient information. URL doesn't work

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• RRID-Legacy
• 6 years ago - submitted by Yufeng Zhao

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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• 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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• 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

Software tool for detection threshold aware CNV calling in matched whole exome sequencing data.

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• SciCrunch
• 6 years ago - submitted by Sarah Sandmann

Optimus is a pipeline developed by the Data Coordination Platform (DCP) of the Human Cell Atlas (HCA) Project that supports processing of any 3' single-cell and single-nuclei expression data generated with the 10x Genomic v2 or v3 assay. It is an alignment and transcriptome quantification pipeline that corrects cell barcodes, aligns reads to the genome, corrects Unique Molecular Identifiers (UMIs), generates an expression matrix in a UMI-aware manner, calculates summary metrics for genes and cells, detects empty droplets, returns read outputs in BAM format, and returns gene counts in NumPy matrix and Loom matrix formats.

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• RRID-Legacy
• 6 years ago - by Anonymous

Software tool as fully integrated online platform for performing systematic reviews of preclinical studies.

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• 6 years ago - submitted by Alexandra Bannach-Brown

Open source community driven guide to reproducible, ethical, inclusive and collaborative data science. Provides information that data scientists in academia, industry and government need at start of their projects to ensure that they are easy to reproduce and reuse at the end. Expanded to series of books covering reproducible research, project design, communication, collaboration, and ethical research.

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• SciCrunch
• 6 years ago - submitted by Anita Bandrowski

Web service that conducts comprehensive literature mining to identify roles of genes in addiction. Searches PubMed to find abstracts containing genes of interest and list of curated addiction related keywords.

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• RRID-Legacy
• 6 years ago - submitted by Hao Chen

Software tool to introduce gene set enrichment for mathematical biology. Measures association between disease of interest and set of genes related to biological pathway. Used for defining gene contributions based on biophysical properties, by leveraging mathematical models of biology to predict effects of genetic perturbations on particular downstream function.

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• RRID-Legacy
• 6 years ago - submitted by Amy Cochran

Spike sorting software for multi day recordings from high channel count probes during electrophysiology experiments.

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

Software tool to construct 3D models of soft tissue using CT-like cross sectional imaging.

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

Open source 3D printing software which supports multi part printing and has slicers.

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