Pluto Bio • Learning Series : Resources and Blog

Resources: Learning series

Informational articles about algorithms, analyses, and visualizations in computational biology and bioinformatics.

The importance of considering covariates in RNA-seq and other -omics data analysis

To draw accurate and meaningful conclusions from RNA-seq data, it is essential to consider covariates, which are additional, potentially “hidden” variables that may impact gene expression in your experiment

Learning Series3 min read

The Origins, Comparisons, and Practical Insights into PRO-seq Technology

Dive into the world of Precision Run-On sequencing (PRO-seq) in this comprehensive blog post. Discover the origins of PRO-seq, how it compares with traditional RNA-seq, and explore a step-by-step guide on conducting a PRO-seq experiment. Uncover how this innovative technology is advancing our understanding of transcriptional dynamics and revolutionizing genomic research.

Learning Series4 min read

Navigating RNA-Seq Data: A Comprehensive Guide to Normalization Methods

RNA sequencing (RNA-Seq) has revolutionized the way we study gene expression. The data deluge it produces, however, presents a critical question: how can we make valid comparisons between different samples or conditions?

Learning Series6 min read

Understanding Key File Formats in High-Throughput Research

Learn about key file formats in high-throughput research, including FASTQ, FASTA, BAM/SAM, BAI, SAM, VCF, GFF/GTF, BED, BedGraph, BigWig, and PDB. Discover how each format is used, what information it contains, and its significance in analyzing ChIP-seq and ATAC-seq data. Understanding these formats is crucial for efficiently handling and analyzing high-throughput data, enabling valuable biological insights and discoveries.

Learning Series3 min read

Accelerating Research Discovery with Bioinformatics Platforms: The Benefits of Implementation

In the field of genomics and bioinformatics, research discovery can be slowed down by the time and resources required to analyze and interpret large datasets. Bioinformatics platforms, which are specialized software or online tools that provide a range of analysis functions, can help to streamline the process and accelerate research discovery.

Learning Series4 min read

CUT&RUN 101 for Biologists

Curious about CUT&RUN and when you would use it? Learn more in this Pluto blog post about getting started with CUT&RUN.

Learning Series3 min read

Exploring the Differences Between Computational Biology and Bioinformatics

This blog post explains the differences between computational biology and bioinformatics. Bioinformatics is concerned with the development and application of computational methods for analyzing and interpreting large biological datasets, while computational biology involves mathematical models and computer simulations to study complex biological systems and processes. The post also describes the different tools and platforms used in each field and how modern SaaS platforms are bringing the two fields together. Finally, a top 10 list summarizes the main differences between computational biology and bioinformatics.

Learning Series3 min read

The Importance of Kaplan-Meier Curves in Computational Biology Research

Kaplan-Meier curves are an essential tool in computational biology research, allowing analysis of survival data and identification of important genes and pathways associated with specific traits or diseases. Learn more about their importance in this blog post. #computationalbiology #KaplanMeier #survivalanalysis

Learning Series2 min read

What is RSEM?

A mini intro to RSEM, a workhorse in RNA-seq data quantification.

Learning Series4 min read

Dimensionality Reduction Techniques in Computational Biology: Insights, origins, and Emerging Directions

Unlocking the power of big data in biology with dimensionality reduction techniques. Explore how PCA, t-SNE, and other methods are driving insights in computational biology. #DimensionalityReduction #ComputationalBiology #BigDataInsights

Learning Series4 min read

Visualizing Genomic Data with IGV Plots: A Powerful Tool for Genomic Research

Discover the power of Integrative Genomics Viewer (IGV) plots - a highly customizable and interactive tool for visualizing and exploring genomic data. Learn how IGV plots can be used in genomic research and the methods for creating data used in these plots. #genomics #bioinformatics.

Learning Series3 min read

Differential Expression Analysis: Understanding the Techniques and Benefits in Research

Differential expression analysis is a powerful tool used to identify genes or transcripts that are differentially expressed between two or more conditions or sample types. This technique is commonly used in the field of genomics, transcriptomics, and proteomics to study the molecular mechanisms underlying different biological processes, such as disease development, response to treatment, or adaptation to different environments.

Learning Series2 min read

Understanding Z-scores in RNA-seq Analysis

In this blog post we will explain what Z-scores are how they are calculated and how they can be used in RNA-seq analysis.

Learning Series3 min read

Revolutionizing Gene Expression: The Power of qPCR

qPCR has transformed molecular biology by providing unparalleled accuracy and sensitivity in the detection and quantification of nucleic acid sequences. Despite its potential drawbacks, such as cost and optimization requirements, qPCR has proven invaluable in research, clinical diagnostics, and food safety testing. Recent advancements in qPCR technology, such as Digital PCR and CRISPR-based qPCR, have further expanded its applications. Learn more about the origins and potential of qPCR in our latest blog post.

Learning Series2 min read

Unraveling the Power of ChIP-seq: A Guide to Understanding Protein-DNA Interactions

ChIP-seq, or chromatin immunoprecipitation sequencing, is a powerful tool used to study protein-DNA interactions in the genome.

Learning Series2 min read

Understanding Fraction and Reads in Peaks: A Guide for ChIP-seq and ATAC-seq Analysis

We will explain what these factors are and how they are used to analyze ChIP-seq and ATAC-seq data

Learning Series2 min read

Exploring the Power of ATAC-seq: A Guide to Understanding Chromatin Accessibility

ATAC-seq, or assay for transposase-accessible chromatin sequencing, is a powerful tool used to study the accessibility of the genome.

Learning Series2 min read

DESeq2: An Overview of a Popular RNA-Seq Analysis Package

DESeq2 is a popular and widely used package in the field of bioinformatics for the analysis of RNA-Seq data. It provides a more comprehensive view of gene expression compared to traditional microarray technology.

Learning Series1 min read

Unleashing the Power of Next-Generation Sequencing (NGS) with the Right Software

Next-generation sequencing (NGS) is a powerful tool used to generate high-throughput DNA sequencing data.

Learning Series2 min read

Cytokine Panels: An In-Depth Guide to Analysis and Significance

Cytokines are small proteins that play a crucial role in regulating the immune system, inflammation, and cell growth.

Learning Series1 min read

An Introduction to SAMtools: A Powerful Tool for Analyzing Next-Generation Sequencing Data

SAMtools is a software package for interacting with and processing next-generation sequencing data

Learning Series2 min read

Trimming RNA-seq Data: A Step-by-Step Guide

In this blog post, we will walk through the steps of trimming RNA-seq data using popular software tools such as Trimmomatic and Cutadapt.

Learning Series2 min read

Understanding the Role of Bioinformatics Engineers

Mastering Key Skills and Coding Languages for Effective Analysis of Biological Data: A Guide to Bioinformatics Engineering