Evaluation of sensitivity and accuracy of widely used scoring functions Sequest, MaxQuant, Peaks, and Byonic. Spectra from E. coli were matched to human sequences, and human spectra from K052 cells were matched to A. loki sequences to determine specificity of matching and FDR estimation. A subsampling analysis of SCX-RP fractionation was performed.

Description from Zenodo: "Objective. This work aims to generate realistic anatomical deformations from static patient scans. Specifically, we present a method to generate these deformations/augmentations via deep learning driven respiratory motion simulation that provides the ground truth for validating deformable image registration (DIR) algorithms and driving more accurate deep learning based...

Description from GitHub: "The goal of mmsig is to provide a flexible and easily interpretable mutational signature analysis tool. mmsig was developed for hematological malignancies, but can be extended to any cancer with a well-known mutational signature landscape. mmsig is based on an expectation maximization algorithm for mutational signature fitting and applies cosine similarities for dynamic...

Description from GitHub: "The gGnome package provides a flexible, queriable R interface to graphs and walks of reference genomic intervals. gGnome is written in the R6 object oriented standard and built around a powerful GenomicRanges, data.table, and igraph backend, and thus supports agile interaction with graphs consisting of hundreds of thousands of nodes and edges."

Description from GitHub: "The goal of fragCounter is to correct Whole genome or targeted sequencing data for GC and mappability bias. The GC bias curve is determined by loess regression of read count by GC and mappability scores. Segmentation is done by circular binary segmentation (CBS) algorithm after getting tumor/normal ratios of corrected read counts."

Description from GitHub: "GenomicRanges-based classes for representing, querying, and manipulating matrices of genomic data (ie a map of pairs of genomic coordinates to a numeric value). Applications include visualization and analysis of Hi-C contact maps, barcode overlap in 10X, microhomology heatmaps, pairwise LD, and epistasis."

Description from GitHub: "General purpose mskilab R tools: R miscellaneous utilities for basic data manipulation, debugging, viz, lsf management, and common mskilab tasks."

Description from GitHub: "R package for plotting tracks of 1D and 2D genomic data stored in GenomicRanges, common UCSC formats, ffTrack. Plotting multiple tracks of complex genomic data across multiple genomic windows."

Code used in the Pointy pipeline from Wan et al. Used to extract point mutations from low-coverage plasma WGS. Available for academic research purposes only

Description from GitHub: "Included in this repository are: 1. CellProfiler pipelines for the segmentation and measurement of cytoplasmic and nuclear fluorescence intensities of ERK-KTR-mClover in confocal time-lapse images of hemizygousÊHprtERK-KTRÊand homozygousÊR26NLS-mKate2Êembryos during pre-implantation development. Pipeline A was used by default and Pipeline B and C were used for cells where...