Bioinformatics, AI, Genomics, Proteomics and Transcriptomics
Determining an appropriate threshold for log2 fold change (log2FC) is a critical step in identifying differentially expressed genes (DEGs) in…
Trimming Illumina reads is a crucial step in preprocessing sequencing data to remove low-quality bases, adapter sequences, and other artifacts.…
Finding common motifs in sequences is a fundamental task in bioinformatics, particularly for identifying conserved regions in DNA, RNA, or…
The PAM50 gene set is a widely used panel of 50 genes for classifying breast cancer subtypes. While the gene…
Running bioinformatics tools like Picard can sometimes lead to “out of disk space” errors, even when you have ample storage.…
Communicating complex bioinformatics concepts to non-computational biologists (NCBs) can be challenging. This guide provides practical tips and strategies to bridge…
Merging multiple FASTQ files into a single file is a common task in bioinformatics, especially when dealing with data from…
When working with human DNA reference files, you may encounter differences in chromosome naming conventions, particularly the presence or absence…
Handling very large datasets is a common challenge in bioinformatics. This guide provides a comprehensive approach to managing and analyzing…
Academic software often comes with a reputation for being difficult to install. This guide explores the reasons behind this challenge,…
Ancestral allele information is crucial for understanding the evolutionary context of genetic variants. This guide provides a detailed protocol for…
Bioinformatics, the intersection of biology and computational science, has revolutionized our ability to analyze and interpret biological data. However, with…
Next-Generation Sequencing (NGS) generates massive amounts of data, often in the form of FASTQ files, which can be several gigabytes…
The Genomic Data Commons (GDC) is the primary repository for The Cancer Genome Atlas (TCGA) data. This guide provides a…
Creating high-quality websites for bioinformatics applications requires a combination of robust backend frameworks, modern frontend libraries, and user-friendly design principles.…
Mapping SNPs to nearby genes is a common task in genomics, especially when studying the potential impact of non-coding variants.…
Principal Component Analysis (PCA) is a powerful tool for analyzing population structure and genetic variation using VCF (Variant Call Format)…
This guide provides a comprehensive approach to retrieving allele frequencies from the 1000 Genomes Project using various tools and programming…
Processing SFF and FastQ files efficiently is a common task in bioinformatics. Below is a step-by-step guide to efficiently view, analyze, clip ends, convert,…
In RNA-seq (and other sequencing technologies like whole-genome sequencing), the terms Read and Fragment are often used, and they have distinct meanings. Here’s a…