Curator Dashboard

Web application providing transmembrane topology prediction. Server incorporates topology information from existing experimental and computational sources using the probabilistic framework of hidden Markov model. Provides the option to precede the topology prediction with signal peptide prediction and transmembrane globular protein discrimination. Given the amino acid sequence of a putative α helical transmembrane protein, CCTOP predicts its topology i.e. localization of membrane spanning regions and orientation of segments between them.

• Resource
• RRID-Legacy
• 8 years ago - by Anonymous

Software tool to provide fast all in one preprocessing for FastQ files. Developed in C++ with multithreading supported to afford high performance. Performs quality control, adapter trimming, quality filtering, per read quality pruning and many other operations with a single scan of the FASTQ data.

• Resource
• SciCrunch
• 8 years ago - submitted by Julien Bane

Software tools to make developing R packages easier by providing R functions that simplify and expedite common tasks.

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• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Software R package for making and manipulating transcript centric annotations. Used to download the genomic locations of the transcripts, exons and cds of a given organism, from either the UCSC Genome Browser or a BioMart database.

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• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Software tool as a full probabilistic model for mapping ancient methylomes using sequencing data underlying an ancient specimen.

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• SciCrunch
• 8 years ago - submitted by kristian hanghoej

Portal for Science Dynamics projects with open source framework to provide way to query datasets. Code framework, including tutorials for project, titled Over Optimization of Academic Publishing Metrics Observing Goodhart Law in Action, to interactively explore and understand how various properties of journals have changed over time. Datasets, software implementations, code tutorials and interactive web interface for investigating studied networks.

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• SciCrunch
• 8 years ago - submitted by Michael Fire

Pipeline for the analysis of 10x single cell RNA sequencing data. Collection of python3 pipelines and Rscripts to analyze data generated with the 10x Genomics platform. The pipelines are based on 10x's Cell Ranger pipeline for mapping and quantitation and the R Seurat package for downstream analysis.

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• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Manually curated collection of human epigenetic factors, their complexes, corresponding genes and products.

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• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Software tool to provide an estimation of the abundances of member cell types in a mixed cell population, using gene expression data. Used for characterizing cell composition of complex tissues from their gene expression profiles, large scale analysis of RNA mixtures for cellular biomarkers and therapeutic targets.

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• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Software written in R for determining cluster count and membership by stability evidence in unsupervised analysis. Provides quantitative and visual stability evidence for estimating the number of unsupervised classes in a dataset with item tracking, item consensus and cluster consensus plots.

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• SciCrunch
• 8 years ago - submitted by Edyta Vieth

ImageJ plugins and macros for whisker tracking. Set of Fiji plugins and macros for tracking a single whisker.

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• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Software tool for vector illustrations. Professional graphic design software.

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• RRID-Legacy
• 8 years ago - by Anonymous

Software tool for professional photo editing.

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• RRID-Legacy
• 8 years ago - by Anonymous

Software tool to create spreadsheets that include tables and images. You can use Apple Pencil on your iPad to add diagrams and colorful illustrations.

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• RRID-Legacy
• 8 years ago - by Anonymous

Software package for efficient manipulation of biological strings. Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences.

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• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Software R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data. Works for read alignments based on transcript coordinates.

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• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Software tool for analysis of sequencing data from ribosome profiling experiments. Used for plotting functions, frameshift detection and parsing of sequencing data from ribosome profiling experiments.

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• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Software tool to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files for directional, non-directional or paired-end sequencing. Wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for Reduced Representation Bisulfite Sequencing data.

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• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Software R package for sequence alignment and counting for R. Used for analyses of second and third generation sequencing data, for read mapping, read counting, SNP calling, short and long read alignment, quantification and mutation discovery. Includes assessment of sequence reads, read alignment, read summarization, exon-exon junction detection, fusion detection, detection of short and long indels, absolute expression calling and SNP calling. Can be used with reads generated from any of the major sequencing platforms including Illumina GA/HiSeq/MiSeq, Roche GS-FLX, ABI SOLiD and LifeTech Ion PGM/Proton sequencers.

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

Software package for low-level analyses of single-cell RNA-seq data. Used for quality control, data exploration and normalization, cell cycle phase assignment, identification of highly variable and correlated genes, clustering into subpopulations and marker gene detection.

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