Go to Pluto
All Collections
Reference: Analysis terms & methods
Reference: Analysis terms & methods
Details and useful links to statistical methods and tools used throughout Pluto
28 articles in this collection
Written by
Rani Powers, PhD,
MacKenzie Demmel,
and
Andrew Goodspeed
Statistical tests for comparing groups of samples
Commonly used tests include the t-test, ANOVA, and Kruskal Wallace
Written by
Rani Powers, PhD
Updated over a week ago
SD versus SEM
Choosing the appropriate statistical analysis for your data.
Written by
MacKenzie Demmel
Updated over a week ago
What is fold change?
Ratio that describes a change in a measured value (e.g. gene expression)
Written by
Rani Powers, PhD
Updated over a week ago
Introduction to RNA-seq
RNA sequencing (RNA-seq) is a popular method for measuring gene expression
Written by
Rani Powers, PhD
Updated over a week ago
What QC information does Pluto provide for RNA-seq analysis?
Uploading FASTQs will output a detailed MultiQC report
Written by
Rani Powers, PhD
Updated over a week ago
What is Glimma?
Interactive graphics from limma
Written by
MacKenzie Demmel
Updated over a week ago
Where does variance come from in RNA-seq data?
Differences in measurements between samples in an experiment
Written by
Andrew Goodspeed
Updated over a week ago
What is a reference genome?
A digital nucleic acid database representing a gene set for an idealized organism.
Written by
Rani Powers, PhD
Updated over a week ago
What is EdgeR?
Empirical analysis of differential gene expression (DGE) in R
Written by
MacKenzie Demmel
Updated over a week ago
What is the read-count?
Total amount of reads in a sample
Written by
Rani Powers, PhD
Updated over a week ago
What is RPKM?
Reads per kilobase of transcript per million reads
Written by
Rani Powers, PhD
Updated over a week ago
What is TPM?
Transcripts per million fragments sequenced
Written by
Rani Powers, PhD
Updated over a week ago
What is depth of sequencing?
Total number of reads in a sample.
Written by
Rani Powers, PhD
Updated over a week ago
What is paired-end sequencing?
Technique used to increase the sequence coverage by sequencing a fragment from both ends.
Written by
Rani Powers, PhD
Updated over a week ago
What is multiplexing?
Combining multiple samples into one sequencing experiment
Written by
Rani Powers, PhD
Updated over a week ago
What are adapters?
Specific sequences that are added to the cDNA fragments during RNAseq library preparation
Written by
Rani Powers, PhD
Updated over a week ago
What is voom?
Mean-variance modeling at the observational level
Written by
Rani Powers, PhD
Updated over a week ago
What is DESeq2?
Differential expression analysis package
Written by
Rani Powers, PhD
Updated over a week ago
What is SortMeRNA?
Ribosomal RNA removal tool.
Written by
Rani Powers, PhD
Updated over a week ago
What is FPKM?
Fragments per kilobase of transcript per million reads.
Written by
Rani Powers, PhD
Updated over a week ago
What is RSeQC?
Quality control of RNA-seq data.
Written by
Rani Powers, PhD
Updated over a week ago
What is SAMtools?
A package of utilities to manipulate large RNA-sequencing files in SAM format.
Written by
Rani Powers, PhD
Updated over a week ago
What is RSEM?
Transcript abundance quantification tool
Written by
Rani Powers, PhD
Updated over a week ago
What is Kallisto?
Fast and reliable pseudo-alignment platform
Written by
Rani Powers, PhD
Updated over a week ago
What is STAR?
Spliced Transcripts Alignment to a Reference
Written by
Rani Powers, PhD
Updated over a week ago
What is Trim Galore?
Adapter and quality trimming.
Written by
Rani Powers, PhD
Updated over a week ago
What is a FASTQ file?
A text file that contain the sequence information and quality scores per read
Written by
Rani Powers, PhD
Updated over a week ago
What is FASTQC?
Checks the quality of the raw reads.
Written by
Rani Powers, PhD
Updated over a week ago