Related papers: Biospectrogram: a tool for spectral analysis of bi…
The pathway is a biological term that refers to a series of interactions between molecules in a cell that causes a certain product or a change in the cell. Pathway analysis is a powerful method for gene expression analysis. Through pathway…
Spectropolarimetry, the observation of polarization and intensity as a function of wavelength, is a powerful tool in stellar astrophysics. It is particularly useful for characterizing stars and circumstellar material, and for tracing the…
The rapid development of the DNA nanotechnology field has been facilitated by advances in CAD software. However, as more complex concepts arose, the lag between the needs and software capabilities appeared. Further derailed by manual…
Pathway Tools is a bioinformatics software environment with a broad set of capabilities. The software provides genome-informatics tools such as a genome browser, sequence alignments, a genome-variant analyzer, and comparative-genomics…
X-ray spectroscopy is a powerful technique for the analysis of the energy distribution of X-rays from astrophysical sources. It allows for the study of the properties, composition, and physical processes taking place at the site of…
Spectangular is a GUI based software package written in C++ designed for spectral disentangling on the wavelength scale. The code disentangles spectra of SB1 and SB2 systems and can now also be used also for spectra showing variability. In…
We introduce software for reading, writing and processing fluorescence single-molecule and image spectroscopy data and developing analysis pipelines that unifies various spectroscopic analysis tools. Our software can be used for processing…
Processing high-throughput DNA sequencing data of individuals or populations requires stringing together independent software tools with many parameters, often leading to non-reproducible pipelines and datasets. We developed grenepipe to…
SparseChem provides fast and accurate machine learning models for biochemical applications. Especially, the package supports very high-dimensional sparse inputs, e.g., millions of features and millions of compounds. It is possible to train…
Spectrograms visualize the frequency components of a given signal which may be an audio signal or even a time-series signal. Audio signals have higher sampling rate and high variability of frequency with time. Spectrograms can capture such…
Real time computer control is an essential feature of scanning probe microscopes, which have become essential tools for the characterization and investigation of nanometer scale samples. Most commercial (and some open-source) scanning probe…
Spectrograms are 2D representations of sound that look very different from the images found in our visual world. And natural images, when played as spectrograms, make unnatural sounds. In this paper, we show that it is possible to…
Signal processing (SP) techniques convert DNA and protein sequences into information that lead to successful drug discovery. One must, however, be aware about the difference between information and entropy1. Eight other physical properties…
BioStatFlow is a free web application, useful to facilitate the performance of statistical analyses of "omics", including metabolomics, data using R packages. It is a fast and easy on-line tool for biologists who are not experts in…
The SPectrogram Analysis and Cataloguing Environment (SPACE) tool is an interactive python tool designed to label radio emission features of interest in a time-frequency map (called 'dynamic spectrum'). The program uses Matplotlib's Polygon…
We present an interactive IDL program for viewing and analyzing astronomical spectra in the context of modern imaging surveys. SpecPro's interactive design lets the user simultaneously view spectroscopic, photometric, and imaging data,…
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…
SpectraPy is an Astropy affiliated package for spectroscopic data reduction. It collects algorithms and methods for data reduction of astronomical spectra obtained by through-slits spectrographs. It has been created to fill the gap in…
A critical step of genome sequence analysis is the mapping of sequenced DNA fragments (i.e., reads) collected from an individual to a known linear reference genome sequence (i.e., sequence-to-sequence mapping). Recent works replace the…
Spectroscopy is an indispensable tool in understanding the structures and dynamics of molecular systems. However computational modelling of spectroscopy is challenging due to the exponential scaling of computational complexity with system…