相关论文: pgMAP: a pipeline to enable guide RNA read mapping…

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…

Background: With the rapid growth of massively parallel sequencing technologies, still more laboratories are utilizing sequenced DNA fragments for genomic analyses. Interpretation of sequencing data is, however, strongly dependent on…

Summary: Mapping ancient DNA to a reference genome is challenging as it involves numerous steps, is time-consuming and has to be repeated within a study to assess the quality of extracts and libraries; as a result, the mapping needs to be…

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…

We present the first public release of ShapePipe, an open-source and modular weak-lensing measurement, analysis, and validation pipeline written in Python. We describe the design of the software and justify the choices made. We provide a…

Chemical mapping methods probe RNA structure by revealing and leveraging correlations of a nucleotide's structural accessibility or flexibility with its reactivity to various chemical probes. Pioneering work by Lucks and colleagues has…

There are currently plenty of programs available for mapping short sequences (reads) to a genome. Most of them, however, including such popular and actively developed programs as Bowtie, BWA, TopHat and many others, are based on…

Background Next Generation Sequencing (NGS) has dramatically enhanced our ability to sequence genomes, but not to assemble them. In practice, many published genome sequences remain in the state of a large set of contigs. Each contig…

With the advent of Next-Generation (NG) sequencing, it has become possible to sequence an entire genome quickly and inexpensively. However, in some experiments one only needs to extract and assembly a portion of the sequence reads, for…

A genome read data set can be quickly and efficiently remapped from one reference to another similar reference (e.g., between two reference versions or two similar species) using a variety of tools, e.g., the commonly-used CrossMap tool.…

PyTerrier provides a declarative framework for building and experimenting with Information Retrieval (IR) pipelines. In this demonstration, we highlight several recent pipeline operations that improve their ability to be programmatically…

Many interesting datasets ubiquitous in machine learning and deep learning can be described via graphs. As the scale and complexity of graph-structured datasets increase, such as in expansive social networks, protein folding, chemical…

We describe a flagging and calibration pipeline intended for making quick look images from GMRT data. The package identifies and flags corrupted visibilities, computes calibration solutions and interpolates these onto the target source.…

Manually reading and logging gauge data is time inefficient, and the effort increases according to the number of gauges available. We present a computer vision pipeline that automates the reading of analog gauges. We propose a two-stage CNN…

Single-cell RNA sequencing (scRNA-seq) is widely used to reveal heterogeneity in cells, which has given us insights into cell-cell communication, cell differentiation, and differential gene expression. However, analyzing scRNA-seq data is a…

Reproducibility and sustainability present significant challenges in bioinformatics software development, where rapidly evolving tools and complex workflows often result in short-lived or difficult-to-adapt pipelines. This paper introduces…

Multiplexed imaging data are revolutionizing our understanding of the composition and organization of tissues and tumors. A critical aspect of such tissue profiling is quantifying the spatial relationship relationships among cells at…

The increasing availability of high-quality optical and near-infrared spectroscopic data, as well as advances in modelling techniques, have greatly expanded the scientific potential of spectroscopic studies. However, the software tools…

Single-cell RNA-seq data allow the quantification of cell type differences across a growing set of biological contexts. However, pinpointing a small subset of genomic features explaining this variability can be ill-defined and…

Duplicate marking is a critical preprocessing step in gene sequence analysis to flag redundant reads arising from polymerase chain reaction(PCR) amplification and sequencing artifacts. Although Picard MarkDuplicates is widely recognized as…