Posts by Tags

16s rRNA amplicon

Taxonomic and diversity profiling of the microbiome - 16S rRNA gene amplicon sequence data

1 minute read

Published:

The 16S ribosomal RNA (rRNA) gene of Bacteria codes for the RNA component of the 30S subunit. Different bacterial species have one to multiple copies of the 16S rRNA gene, and each with 9 hypervariable regions, V1-V9. High-throughput sequencing of 16S rRNA gene (a “marker gene”) amplicons has become a widely used method to study bacterial phylogeny and species classification. Read more

DADA2

Taxonomic and diversity profiling of the microbiome - 16S rRNA gene amplicon sequence data

1 minute read

Published:

The 16S ribosomal RNA (rRNA) gene of Bacteria codes for the RNA component of the 30S subunit. Different bacterial species have one to multiple copies of the 16S rRNA gene, and each with 9 hypervariable regions, V1-V9. High-throughput sequencing of 16S rRNA gene (a “marker gene”) amplicons has become a widely used method to study bacterial phylogeny and species classification. Read more

FastQC

GATK

Genomic variants from RNA-Seq data

1 minute read

Published:

RNA-Seq allows the detection and quantification of known and rare RNA transcripts within a sample. In addition to differential expression and detection of novel transcripts, RNA-seq also supports the detection of genomic variation in expressed regions. Read more

HTSeq

HUMAnN2

Indel

Genomic variants from RNA-Seq data

1 minute read

Published:

RNA-Seq allows the detection and quantification of known and rare RNA transcripts within a sample. In addition to differential expression and detection of novel transcripts, RNA-seq also supports the detection of genomic variation in expressed regions. Read more

LFQ

Quantitative proteomics: label-free quantitation of proteins

2 minute read

Published:

Liquid chromatography (LC) coupled with mass spectrometry (MS) has been widely used for protein expression quantification. Protein quantification by tandem-MS (MS/MS) uses integrated peak intensity from the parent-ion mass (MS1) or features from fragment-ions (MS2). MS1 methods use the iBAQ (intensity Based Absolute Quantification) algorithm (a protein’s total non-normalised intensities are divided by the number of measurable tryptic peptides). Untargeted label-free quantitation (LFQ) of proteins, aims to determine the relative amount of proteins in two or more biological samples. Read more

MatrixEqtl

eQTL analysis of RNA-Seq data

less than 1 minute read

Published:

Genetic locus that affects gene expression is often referred to as expression quantitative trait locus (eQTL). eQTL mapping studies assesses the association of SNPs with genome-wide expression levels. Read more

MaxQuant

Quantitative proteomics: label-free quantitation of proteins

2 minute read

Published:

Liquid chromatography (LC) coupled with mass spectrometry (MS) has been widely used for protein expression quantification. Protein quantification by tandem-MS (MS/MS) uses integrated peak intensity from the parent-ion mass (MS1) or features from fragment-ions (MS2). MS1 methods use the iBAQ (intensity Based Absolute Quantification) algorithm (a protein’s total non-normalised intensities are divided by the number of measurable tryptic peptides). Untargeted label-free quantitation (LFQ) of proteins, aims to determine the relative amount of proteins in two or more biological samples. Read more

MetaPhlAn2

OTU

Taxonomic and diversity profiling of the microbiome - 16S rRNA gene amplicon sequence data

1 minute read

Published:

The 16S ribosomal RNA (rRNA) gene of Bacteria codes for the RNA component of the 30S subunit. Different bacterial species have one to multiple copies of the 16S rRNA gene, and each with 9 hypervariable regions, V1-V9. High-throughput sequencing of 16S rRNA gene (a “marker gene”) amplicons has become a widely used method to study bacterial phylogeny and species classification. Read more

PTXQC

Quantitative proteomics: label-free quantitation of proteins

2 minute read

Published:

Liquid chromatography (LC) coupled with mass spectrometry (MS) has been widely used for protein expression quantification. Protein quantification by tandem-MS (MS/MS) uses integrated peak intensity from the parent-ion mass (MS1) or features from fragment-ions (MS2). MS1 methods use the iBAQ (intensity Based Absolute Quantification) algorithm (a protein’s total non-normalised intensities are divided by the number of measurable tryptic peptides). Untargeted label-free quantitation (LFQ) of proteins, aims to determine the relative amount of proteins in two or more biological samples. Read more

Perseus

Quantitative proteomics: label-free quantitation of proteins

2 minute read

Published:

Liquid chromatography (LC) coupled with mass spectrometry (MS) has been widely used for protein expression quantification. Protein quantification by tandem-MS (MS/MS) uses integrated peak intensity from the parent-ion mass (MS1) or features from fragment-ions (MS2). MS1 methods use the iBAQ (intensity Based Absolute Quantification) algorithm (a protein’s total non-normalised intensities are divided by the number of measurable tryptic peptides). Untargeted label-free quantitation (LFQ) of proteins, aims to determine the relative amount of proteins in two or more biological samples. Read more

Proteomics

Quantitative proteomics: label-free quantitation of proteins

2 minute read

Published:

Liquid chromatography (LC) coupled with mass spectrometry (MS) has been widely used for protein expression quantification. Protein quantification by tandem-MS (MS/MS) uses integrated peak intensity from the parent-ion mass (MS1) or features from fragment-ions (MS2). MS1 methods use the iBAQ (intensity Based Absolute Quantification) algorithm (a protein’s total non-normalised intensities are divided by the number of measurable tryptic peptides). Untargeted label-free quantitation (LFQ) of proteins, aims to determine the relative amount of proteins in two or more biological samples. Read more

RNA-Seq

Genomic variants from RNA-Seq data

1 minute read

Published:

RNA-Seq allows the detection and quantification of known and rare RNA transcripts within a sample. In addition to differential expression and detection of novel transcripts, RNA-seq also supports the detection of genomic variation in expressed regions. Read more

eQTL analysis of RNA-Seq data

less than 1 minute read

Published:

Genetic locus that affects gene expression is often referred to as expression quantitative trait locus (eQTL). eQTL mapping studies assesses the association of SNPs with genome-wide expression levels. Read more

RNASeq

RawMeat

Quantitative proteomics: label-free quantitation of proteins

2 minute read

Published:

Liquid chromatography (LC) coupled with mass spectrometry (MS) has been widely used for protein expression quantification. Protein quantification by tandem-MS (MS/MS) uses integrated peak intensity from the parent-ion mass (MS1) or features from fragment-ions (MS2). MS1 methods use the iBAQ (intensity Based Absolute Quantification) algorithm (a protein’s total non-normalised intensities are divided by the number of measurable tryptic peptides). Untargeted label-free quantitation (LFQ) of proteins, aims to determine the relative amount of proteins in two or more biological samples. Read more

SNP

Genomic variants from RNA-Seq data

1 minute read

Published:

RNA-Seq allows the detection and quantification of known and rare RNA transcripts within a sample. In addition to differential expression and detection of novel transcripts, RNA-seq also supports the detection of genomic variation in expressed regions. Read more

STAR

Genomic variants from RNA-Seq data

1 minute read

Published:

RNA-Seq allows the detection and quantification of known and rare RNA transcripts within a sample. In addition to differential expression and detection of novel transcripts, RNA-seq also supports the detection of genomic variation in expressed regions. Read more

cnv

computing

Taxonomic and diversity profiling of the microbiome - 16S rRNA gene amplicon sequence data

1 minute read

Published:

The 16S ribosomal RNA (rRNA) gene of Bacteria codes for the RNA component of the 30S subunit. Different bacterial species have one to multiple copies of the 16S rRNA gene, and each with 9 hypervariable regions, V1-V9. High-throughput sequencing of 16S rRNA gene (a “marker gene”) amplicons has become a widely used method to study bacterial phylogeny and species classification. Read more

curation

discordant sex informaion

Quality control for GWAS studies

1 minute read

Published:

An important step in the analysis of genome-wide association studies (GWAS) is to identify problematic subjects and markers. Quality control (QC) in GWAS removes markers and individuals, and greatly increases the accuracy of findings. Read more

eQTL

eQTL analysis of RNA-Seq data

less than 1 minute read

Published:

Genetic locus that affects gene expression is often referred to as expression quantitative trait locus (eQTL). eQTL mapping studies assesses the association of SNPs with genome-wide expression levels. Read more

edgeR

eQTL analysis of RNA-Seq data

less than 1 minute read

Published:

Genetic locus that affects gene expression is often referred to as expression quantitative trait locus (eQTL). eQTL mapping studies assesses the association of SNPs with genome-wide expression levels. Read more

functional profiling

genomics

heterozygosity rate

Quality control for GWAS studies

1 minute read

Published:

An important step in the analysis of genome-wide association studies (GWAS) is to identify problematic subjects and markers. Quality control (QC) in GWAS removes markers and individuals, and greatly increases the accuracy of findings. Read more

htseq

eQTL analysis of RNA-Seq data

less than 1 minute read

Published:

Genetic locus that affects gene expression is often referred to as expression quantitative trait locus (eQTL). eQTL mapping studies assesses the association of SNPs with genome-wide expression levels. Read more

human complement

iBAC

Quantitative proteomics: label-free quantitation of proteins

2 minute read

Published:

Liquid chromatography (LC) coupled with mass spectrometry (MS) has been widely used for protein expression quantification. Protein quantification by tandem-MS (MS/MS) uses integrated peak intensity from the parent-ion mass (MS1) or features from fragment-ions (MS2). MS1 methods use the iBAQ (intensity Based Absolute Quantification) algorithm (a protein’s total non-normalised intensities are divided by the number of measurable tryptic peptides). Untargeted label-free quantitation (LFQ) of proteins, aims to determine the relative amount of proteins in two or more biological samples. Read more

metagenomics

microbiome

Taxonomic and diversity profiling of the microbiome - 16S rRNA gene amplicon sequence data

1 minute read

Published:

The 16S ribosomal RNA (rRNA) gene of Bacteria codes for the RNA component of the 30S subunit. Different bacterial species have one to multiple copies of the 16S rRNA gene, and each with 9 hypervariable regions, V1-V9. High-throughput sequencing of 16S rRNA gene (a “marker gene”) amplicons has become a widely used method to study bacterial phylogeny and species classification. Read more

missingness

Quality control for GWAS studies

1 minute read

Published:

An important step in the analysis of genome-wide association studies (GWAS) is to identify problematic subjects and markers. Quality control (QC) in GWAS removes markers and individuals, and greatly increases the accuracy of findings. Read more

networks

Quality control for GWAS studies

1 minute read

Published:

An important step in the analysis of genome-wide association studies (GWAS) is to identify problematic subjects and markers. Quality control (QC) in GWAS removes markers and individuals, and greatly increases the accuracy of findings. Read more

qiime2

Taxonomic and diversity profiling of the microbiome - 16S rRNA gene amplicon sequence data

1 minute read

Published:

The 16S ribosomal RNA (rRNA) gene of Bacteria codes for the RNA component of the 30S subunit. Different bacterial species have one to multiple copies of the 16S rRNA gene, and each with 9 hypervariable regions, V1-V9. High-throughput sequencing of 16S rRNA gene (a “marker gene”) amplicons has become a widely used method to study bacterial phylogeny and species classification. Read more

runs of homozygosity

Quality control for GWAS studies

1 minute read

Published:

An important step in the analysis of genome-wide association studies (GWAS) is to identify problematic subjects and markers. Quality control (QC) in GWAS removes markers and individuals, and greatly increases the accuracy of findings. Read more

shotgun metagenomics sequencing

taxonomic profiling