Curator Dashboard

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.

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• 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.

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• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Software package of python scripts made to simplify the processing of crystal diffraction images.

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• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Software tool as an algorithm to infer gene regulatory networks from spatial and temporal datasets. Spatial dataset or any data that can provide information about coexpression is used by the first step of the algorithm to perform clustering and separate the genes in the network in smaller coexpressed groups. Temporal dataset is used by the second step of the algorithm to infer regulations among the genes, based on Bayesian networks.

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• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Web tool for synthetic single-guide RNA design of CRISPR-system in plants. Allows to search for high specificity Cas9 target sites within DNA sequences of interest, which also provides off-target loci prediction for specificity analyses and marks restriction enzyme cutting site to every sgRNA for further convenient in experiment.

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• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Test for UMICH

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• SciCrunch
• 8 years ago - submitted by Isabella Froman

Software tool for data analysis and exploration. Statistics software for Mac.

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• RRID-Legacy
• 8 years ago - by Anonymous

Software tool to annotate structural variant calls with sequence depth information that can add or remove confidence to SV predicted to affect copy number. Indicates the presence of a rapid change in depth relative to the regions surrounding the breakpoints. Allows the run time to be nearly independent of the number of variants important for large, jointly called projects with many samples. Annotates structural variant predictions made from both short read and long read data.

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• SciCrunch
• 8 years ago - submitted by Brent Pedersen