Related papers: Portable-CELLxGENE: standalone executables of CELL…
The CellxGene project has enabled access to single-cell data in the scientific community, providing tools for browsed-based no-code analysis of more than 500 annotated datasets. However, single-cell data requires dimensional reduction to…
Motivation: Bioinformatics software often lacks graphical user interfaces (GUIs), which can limit its adoption by non-technical members of the scientific community. Web interfaces are a common alternative for building cross-platform GUIs,…
CellProfiler is a widely used software for creating reproducible, reusable image analysis workflows without needing to code. In addition to the >90 modules that make up the main CellProfiler program, CellProfiler has a plugins system that…
Developing complex biomolecular workflows is not always straightforward. It requires tedious developments to enable the interoperability between the different biomolecular simulation and analysis tools. Moreover, the need to execute the…
The cell cycle is one of the most fundamental biological processes important for understanding normal physiology and various pathologies such as cancer. Single cell RNA sequencing technologies give an opportunity to analyse the cell cycle…
The computer programs most users interact with daily are driven by a graphical user interface (GUI). However, many scientific applications are used with a command line interface (CLI) for the ease of development and increased flexibility…
The UCSC Genome Browser is a popular tool for the exploration and analysis of reference genomes. Mirrors of the UCSC Genome Browser and its contents exist at multiple geographic locations, and this mirror procedure has been modified to…
RNA sequencing techniques, like bulk RNA-seq and Single Cell (sc) RNA-seq, are critical tools for the biologist looking to analyze the genetic activity/transcriptome of a tissue or cell during an experimental procedure. Platforms like…
Single-cell RNA sequencing (scRNA-seq) has transformed our ability to explore biological systems. Nevertheless, proficient expertise is essential for handling and interpreting the data. In this paper, we present scX, an R package built on…
We introduce cellanneal, a python-based software for deconvolving bulk RNA sequencing data. cellanneal relies on the optimization of Spearman's rank correlation coefficient between experimental and computational mixture gene expression…
Cell identity encompasses various semantic aspects of a cell, including cell type, pathway information, disease information, and more, which are essential for biologists to gain insights into its biological characteristics. Understanding…
Constructing cell developmental trajectories is a critical task in single-cell RNA sequencing (scRNA-seq) analysis, enabling the inference of potential cellular progression paths. However, current automated methods are limited to…
Motivation: Networks underlie the generation and interpretation of many biological datasets: gene networks shed light on the regulatory structure of the genome, and cell networks can capture structure of the tumor micro-environment.…
Single-cell technologies have revolutionized biomedical research by enabling scalable measurement of the genome, transcriptome, and proteome of multiple systems at single-cell resolution. Now widely applied to cancer models, these assays…
Most particle induced X-ray emission (PIXE) data analysis codes are not focused on handling multilayered samples. We have developed an open-source library called "LibCPIXE", for PIXE data analysis. It is written in standard C and implements…
SMeagol is a software tool to simulate highly realistic microscopy data based on spatial systems biology models, in order to facilitate development, validation, and optimization of advanced analysis methods for live cell single molecule…
GenoML is a Python package automating machine learning workflows for genomics (genetics and multi-omics) with an open science philosophy. Genomics data require significant domain expertise to clean, pre-process, harmonize and perform…
Portable genome sequencing technology is revolutionizing genomic research by providing a faster, more flexible method of sequencing DNA and RNA [1, 2]. The unprecedented shift from bulky stand-alone benchtop equipment confined in a…
The oxDNA model of DNA has been applied widely to systems in biology, biophysics and nanotechnology. It is currently available via two independent open source packages. Here we present a set of clearly-documented exemplar simulations that…
A low cost remote imaging platform for biological applications was developed. The "Picroscope" is a device that allows the user to perform longitudinal imaging studies on multi-well cell culture plates. Here we present the network…