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: "Recent studies have revealed diverse amino acid, post-translational and non-canonical modifications of proteins in diverse organisms and tissues. However, their unbiased detection and analysis remain hindered by technical limitations. Here, we present a spectral alignment method for the identification of protein modifications from high-resolution tandem peptide mass spectrometry....

Description from Zenodo: "So yoU think you Found A Mutation (SUFAM)? SUFAM reports the mutant allele fraction (MAF), read counts and coverage of a given variant or mutation in a SAM/BAM/CRAM file. It is a Python wrapper around samtools mpileup that makes it straightforward to determine the MAF of a given mutation. Parsing the output of samtools mpileup is error prone, while SUFAM has been rigorously...

Description from Zenodo: "This repository contains experimental data and code supporting the publication: Li et al. (2020) Single-gene imaging links genome topology, promoter–enhancer communication and transcription control. Nat. Struct. Mol. Biol., DOI:https://doi.org/10.1038/s41594-020-0493-6 Details about the files are provided in the Readme files in the associated sub-folders."

Code associated with the manuscript for "Gene interaction network analysis in multiple myeloma detects complex immune dysregulation associated with shorter survival." Includes data and instructions, R scripts, lab notebooks, and high resolution images.

Custom genomic resource files for Mouse Variant pipeline. The pipeline itself can be found via the GitHub link.

Description from GitHub: "This is a collection of miscellaneous wrappers for pipelining and processing genomic data. In addition there are utilities for quick interactive programming."

Description from GitHub: "Schrödinger project files, YANK simulation inputs, and analysis scripts from 'Small-molecule targeting of MUSASHI RNA-binding activity in acute myeloid leukemia'."

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: "Mapping gene expression cartography from spatial transcriptomics for tissues with stereotypical structures. What's new? We developed a new doising method using data diffusion over the imputed SpaceFold axis to oversome sparsity of Visium data and further improve the resolution of cartography over the sliding window mean used by the v1.0 (the SpaceFold paper). The new...