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Uterine Cervix and Corpus Cancers Characterization Through Gene Expression Analysis Using the KnowSeq Tool
The characterization of cancer through gene expression quantification data analysis is a powerful and widely used approach in cancer research. This...
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SubCellBarCode: integrated workflow for robust spatial proteomics by mass spectrometry
The molecular functions of a protein are defined by its inherent properties in relation to its environment and interaction network. Within a cell,...
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IMMAN: an R/Bioconductor package for Interolog protein network reconstruction, map** and mining analysis
BackgroundReconstruction of protein-protein interaction networks (PPIN) has been riddled with controversy for decades. Particularly, false-negative...
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MBECS: Microbiome Batch Effects Correction Suite
Despite the availability of batch effect correcting algorithms (BECA), no comprehensive tool that combines batch correction and evaluation of the...
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FastqCleaner: an interactive Bioconductor application for quality-control, filtering and trimming of FASTQ files
BackgroundExploration and processing of FASTQ files are the first steps in state-of-the-art data analysis workflows of Next Generation Sequencing...
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Introduction to R for Microbiome Data
This chapter first introduces some useful R functions and R packages for microbiome data. Then it illustrates some specifically designed R packages...
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RegEnrich gene regulator enrichment analysis reveals a key role of the ETS transcription factor family in interferon signaling
Changes in a few key transcriptional regulators can lead to different biological states. Extracting the key gene regulators governing a biological...
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HPAanalyze: an R package that facilitates the retrieval and analysis of the Human Protein Atlas data
BackgroundThe Human Protein Atlas (HPA) aims to map human proteins via multiple technologies including imaging, proteomics and transcriptomics....
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Identification of Genes Post-Transcriptionally Regulated from RNA-seq: The Case Study of Liver Hepatocellular Carcinoma
The field of transcriptional regulation generally assumes that changes in transcripts levels reflect changes in transcriptional status of the...
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SigsPack , a package for cancer mutational signaturesBackgroundMutational signatures are specific patterns of somatic mutations introduced into the genome by oncogenic processes. Several mutational...
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Exploring Protein Interactome Data with IPinquiry: Statistical Analysis and Data Visualization by Spectral Counts
Immunoprecipitation mass spectrometry (IP-MS) is a popular method for the identification of protein-protein interactions. This approach is...
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scAnnotatR: framework to accurately classify cell types in single-cell RNA-sequencing data
BackgroundAutomatic cell type identification is essential to alleviate a key bottleneck in scRNA-seq data analysis. While most existing...
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Current Status and Future Strategy in Crop Improvement Using Epigenomics
Rapidly increasing population demands high yield of crops whereas the area under cultivation is decreasing with increased population. Also, the...
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ORdensity: user-friendly R package to identify differentially expressed genes
BackgroundMicroarray technology provides the expression level of many genes. Nowadays, an important issue is to select a small number of informative...
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Performing QTL and eQTL Analyses with the R-Package GenomicTools
We present the R-package GenomicTools that can be used to perform QTL and eQTL analyses in a user-friendly way. First, the theoretical backgrounds of...
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recount3: summaries and queries for large-scale RNA-seq expression and splicing
We present recount3, a resource consisting of over 750,000 publicly available human and mouse RNA sequencing (RNA-seq) samples uniformly processed by...
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Rescuing biologically relevant consensus regions across replicated samples
BackgroundProtein-DNA binding sites of ChIP-seq experiments are identified where the binding affinity is significant based on a given threshold. The...
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Multi-omics Data Integration in the Context of Plant Abiotic Stress Signaling
In order to answer new biological questions, high-throughput data generated by new biotechnologies can be very meaningful but require specific and...
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Statistical and Biological Data Analysis Using Programming Languages
Rapid progress in high throughput sequencing technologies has generated an unprecedented huge amount of complex and heterogeneous biological data and...
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Big Data Analysis
Big data is a term applicable to data that are too large or complex for traditional data-processing...