Spatial gene expression data analysis on Cluster (10X Genomics, Space Ranger)
Published:
Running spaceranger as cluster mode that uses Sun Grid Engine (SGE) as queuing.
Published:
Running spaceranger as cluster mode that uses Sun Grid Engine (SGE) as queuing.
Published:
Updated on May 03, 2021
Published:
Quantification of proteins using isobaric labeling (tandem mass tag or TMT) starts with the reduction of disulfide bonds in proteins with Dithiothreitol (DTT).
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.
Published:
ATAC-seq (Assay for Transposase Accessible Chromatin with high-throughput Sequencing) is a next-generation sequencing approach for the analysis of open chromatin regions to assess the genome-wise chromatin accessibility.
Published:
Updated on September 13, 2021
Published:
ATAC-seq (Assay for Transposase Accessible Chromatin with high-throughput Sequencing) is a next-generation sequencing approach for the analysis of open chromatin regions to assess the genome-wise chromatin accessibility.
Published:
Kaplan-Meier curve shows what the probability of an event (for example, survival) at a certain time interval. The log-rank test compares the survival curves of two or more groups. With a small subset of patients, the Kaplan-Meier estimates can be misleading and should be interpreted with caution.
Published:
Tools such as ANNOVAR, Variant Effect Predictor (VEP) or SnpEff annotate genetic variants (SNPs, INDELS, CNVs etc) present in VCF file. These tools integrate the annotations within the INFO column of the original VCF file.
Published:
Quantification of proteins using isobaric labeling (tandem mass tag or TMT) starts with the reduction of disulfide bonds in proteins with Dithiothreitol (DTT).
Published:
Updated on September 13, 2021
Published:
Updated on May 03, 2021
Published:
Updated on May 03, 2021
Published:
Running spaceranger as cluster mode that uses Sun Grid Engine (SGE) as queuing.
Published:
Updated on May 03, 2021
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.
Published:
The aptamer-based SomaScan® assay is one of the popular methods of measuring abundances of protein targets. There is very little information on correlation between mass spectrometry (MS)-based proteomics, SOMAscan and Olink assays; Olink is another popular high throughput antibody-based platform. Some studies also reported a measurement variation between those platforms. In general aptamers/SOMAmers are selected against target proteins in their native conformation and in some cases against a functional protein with “known” post translational modifications (PTMs). It’s well known that novel PTMs (pathogen or disease-induced) can impact the protein structure, electrophilicity and interactions with proteins. The other main disadvantage is quantification which is based on DNA microarray chips (background noise). The main advantages are lower cost and data analysis.
Published:
Kaplan-Meier curve shows what the probability of an event (for example, survival) at a certain time interval. The log-rank test compares the survival curves of two or more groups. With a small subset of patients, the Kaplan-Meier estimates can be misleading and should be interpreted with caution.
Published:
Tools such as ANNOVAR, Variant Effect Predictor (VEP) or SnpEff annotate genetic variants (SNPs, INDELS, CNVs etc) present in VCF file. These tools integrate the annotations within the INFO column of the original VCF file.
Published:
Quantification of proteins using isobaric labeling (tandem mass tag or TMT) starts with the reduction of disulfide bonds in proteins with Dithiothreitol (DTT).
Published:
Updated on September 13, 2021
Published:
A simple RNA-Seq differential expression analysis using High Performance Computing (HPC).
Published:
Updated on May 03, 2021
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.
Published:
Tools such as ANNOVAR, Variant Effect Predictor (VEP) or SnpEff annotate genetic variants (SNPs, INDELS, CNVs etc) present in VCF file. These tools integrate the annotations within the INFO column of the original VCF file.
Published:
Tools such as ANNOVAR, Variant Effect Predictor (VEP) or SnpEff annotate genetic variants (SNPs, INDELS, CNVs etc) present in VCF file. These tools integrate the annotations within the INFO column of the original VCF file.
Published:
ATAC-seq (Assay for Transposase Accessible Chromatin with high-throughput Sequencing) is a next-generation sequencing approach for the analysis of open chromatin regions to assess the genome-wise chromatin accessibility.
Published:
A simple RNA-Seq differential expression analysis using High Performance Computing (HPC).
Published:
This workflow consists of taxonomic and functional profiling of shotgun metagenomics sequencing (MGS) reads using MetaPhlAn2 and HUMAnN2, respectively. To perform taxonomic (phyla, genera or species level) profiling of the MGS data, the MetaPhlAn2 pipeline was run on a high performance multicore cluster computing environment.
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.
Published:
Kaplan-Meier curve shows what the probability of an event (for example, survival) at a certain time interval. The log-rank test compares the survival curves of two or more groups. With a small subset of patients, the Kaplan-Meier estimates can be misleading and should be interpreted with caution.
Published:
Updated on September 13, 2021
Published:
ATAC-seq (Assay for Transposase Accessible Chromatin with high-throughput Sequencing) is a next-generation sequencing approach for the analysis of open chromatin regions to assess the genome-wise chromatin accessibility.
Published:
The aptamer-based SomaScan® assay is one of the popular methods of measuring abundances of protein targets. There is very little information on correlation between mass spectrometry (MS)-based proteomics, SOMAscan and Olink assays; Olink is another popular high throughput antibody-based platform. Some studies also reported a measurement variation between those platforms. In general aptamers/SOMAmers are selected against target proteins in their native conformation and in some cases against a functional protein with “known” post translational modifications (PTMs). It’s well known that novel PTMs (pathogen or disease-induced) can impact the protein structure, electrophilicity and interactions with proteins. The other main disadvantage is quantification which is based on DNA microarray chips (background noise). The main advantages are lower cost and data analysis.
Published:
Quantification of proteins using isobaric labeling (tandem mass tag or TMT) starts with the reduction of disulfide bonds in proteins with Dithiothreitol (DTT).
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.
Based on the hg38 reference genome, paired-end reads are mapped by STAR aligner. The mapped reads are used for expression quantification without assembling transcripts by counting the number of reads that map to an exon by HTSeq that uses Refseq gene annotations. Then, to correct for systematic variability such as library fragment size, sequence composition bias, and read depth the raw counts are normalized as trimmed mean of M-values (TMM) through edgeR.
Published:
Quantification of proteins using isobaric labeling (tandem mass tag or TMT) starts with the reduction of disulfide bonds in proteins with Dithiothreitol (DTT).
Published:
Updated on September 13, 2021
Published:
This workflow consists of taxonomic and functional profiling of shotgun metagenomics sequencing (MGS) reads using MetaPhlAn2 and HUMAnN2, respectively. To perform taxonomic (phyla, genera or species level) profiling of the MGS data, the MetaPhlAn2 pipeline was run on a high performance multicore cluster computing environment.
Published:
Tools such as ANNOVAR, Variant Effect Predictor (VEP) or SnpEff annotate genetic variants (SNPs, INDELS, CNVs etc) present in VCF file. These tools integrate the annotations within the INFO column of the original VCF file.
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.
Published:
The aptamer-based SomaScan® assay is one of the popular methods of measuring abundances of protein targets. There is very little information on correlation between mass spectrometry (MS)-based proteomics, SOMAscan and Olink assays; Olink is another popular high throughput antibody-based platform. Some studies also reported a measurement variation between those platforms. In general aptamers/SOMAmers are selected against target proteins in their native conformation and in some cases against a functional protein with “known” post translational modifications (PTMs). It’s well known that novel PTMs (pathogen or disease-induced) can impact the protein structure, electrophilicity and interactions with proteins. The other main disadvantage is quantification which is based on DNA microarray chips (background noise). The main advantages are lower cost and data analysis.
Published:
Quantification of proteins using isobaric labeling (tandem mass tag or TMT) starts with the reduction of disulfide bonds in proteins with Dithiothreitol (DTT).
Published:
Updated on September 13, 2021
Published:
Quantification of proteins using isobaric labeling (tandem mass tag or TMT) starts with the reduction of disulfide bonds in proteins with Dithiothreitol (DTT).
Published:
Updated on September 13, 2021
Published:
The aptamer-based SomaScan® assay is one of the popular methods of measuring abundances of protein targets. There is very little information on correlation between mass spectrometry (MS)-based proteomics, SOMAscan and Olink assays; Olink is another popular high throughput antibody-based platform. Some studies also reported a measurement variation between those platforms. In general aptamers/SOMAmers are selected against target proteins in their native conformation and in some cases against a functional protein with “known” post translational modifications (PTMs). It’s well known that novel PTMs (pathogen or disease-induced) can impact the protein structure, electrophilicity and interactions with proteins. The other main disadvantage is quantification which is based on DNA microarray chips (background noise). The main advantages are lower cost and data analysis.
Published:
A simple RNA-Seq differential expression analysis using High Performance Computing (HPC).
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.
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.
Based on the hg38 reference genome, paired-end reads are mapped by STAR aligner. The mapped reads are used for expression quantification without assembling transcripts by counting the number of reads that map to an exon by HTSeq that uses Refseq gene annotations. Then, to correct for systematic variability such as library fragment size, sequence composition bias, and read depth the raw counts are normalized as trimmed mean of M-values (TMM) through edgeR.
Published:
A simple RNA-Seq differential expression analysis using High Performance Computing (HPC).
Published:
Running spaceranger as cluster mode that uses Sun Grid Engine (SGE) as queuing.
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.
Published:
The aptamer-based SomaScan® assay is one of the popular methods of measuring abundances of protein targets. There is very little information on correlation between mass spectrometry (MS)-based proteomics, SOMAscan and Olink assays; Olink is another popular high throughput antibody-based platform. Some studies also reported a measurement variation between those platforms. In general aptamers/SOMAmers are selected against target proteins in their native conformation and in some cases against a functional protein with “known” post translational modifications (PTMs). It’s well known that novel PTMs (pathogen or disease-induced) can impact the protein structure, electrophilicity and interactions with proteins. The other main disadvantage is quantification which is based on DNA microarray chips (background noise). The main advantages are lower cost and data analysis.
Published:
Running spaceranger as cluster mode that uses Sun Grid Engine (SGE) as queuing.
Published:
A simple RNA-Seq differential expression analysis using High Performance Computing (HPC).
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.
Published:
Updated on May 03, 2021
Published:
Updated on May 03, 2021
Published:
Updated on May 03, 2021
Published:
Running spaceranger as cluster mode that uses Sun Grid Engine (SGE) as queuing.
Published:
Kaplan-Meier curve shows what the probability of an event (for example, survival) at a certain time interval. The log-rank test compares the survival curves of two or more groups. With a small subset of patients, the Kaplan-Meier estimates can be misleading and should be interpreted with caution.
Published:
Quantification of proteins using isobaric labeling (tandem mass tag or TMT) starts with the reduction of disulfide bonds in proteins with Dithiothreitol (DTT).
Published:
Quantification of proteins using isobaric labeling (tandem mass tag or TMT) starts with the reduction of disulfide bonds in proteins with Dithiothreitol (DTT).
Published:
Tools such as ANNOVAR, Variant Effect Predictor (VEP) or SnpEff annotate genetic variants (SNPs, INDELS, CNVs etc) present in VCF file. These tools integrate the annotations within the INFO column of the original VCF file.
Published:
Tools such as ANNOVAR, Variant Effect Predictor (VEP) or SnpEff annotate genetic variants (SNPs, INDELS, CNVs etc) present in VCF file. These tools integrate the annotations within the INFO column of the original VCF file.
Published:
Tools such as ANNOVAR, Variant Effect Predictor (VEP) or SnpEff annotate genetic variants (SNPs, INDELS, CNVs etc) present in VCF file. These tools integrate the annotations within the INFO column of the original VCF file.
Published:
Running spaceranger as cluster mode that uses Sun Grid Engine (SGE) as queuing.
Published:
Kaplan-Meier curve shows what the probability of an event (for example, survival) at a certain time interval. The log-rank test compares the survival curves of two or more groups. With a small subset of patients, the Kaplan-Meier estimates can be misleading and should be interpreted with caution.
Published:
Tools such as ANNOVAR, Variant Effect Predictor (VEP) or SnpEff annotate genetic variants (SNPs, INDELS, CNVs etc) present in VCF file. These tools integrate the annotations within the INFO column of the original VCF file.
Published:
The aptamer-based SomaScan® assay is one of the popular methods of measuring abundances of protein targets. There is very little information on correlation between mass spectrometry (MS)-based proteomics, SOMAscan and Olink assays; Olink is another popular high throughput antibody-based platform. Some studies also reported a measurement variation between those platforms. In general aptamers/SOMAmers are selected against target proteins in their native conformation and in some cases against a functional protein with “known” post translational modifications (PTMs). It’s well known that novel PTMs (pathogen or disease-induced) can impact the protein structure, electrophilicity and interactions with proteins. The other main disadvantage is quantification which is based on DNA microarray chips (background noise). The main advantages are lower cost and data analysis.
Published:
Running spaceranger as cluster mode that uses Sun Grid Engine (SGE) as queuing.
Published:
Copy number variations (CNVs) represent gain or loss of genomic regions. CNVs transmit from parents to offspring or arise de novo and play important role in neuro-psychiatric disorders and cancers.
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.
Published:
Copy number variations (CNVs) represent gain or loss of genomic regions. CNVs transmit from parents to offspring or arise de novo and play important role in neuro-psychiatric disorders and cancers.
Published:
The human complement activation takes place through one or more of the well-established pathways consisting of plasma and membrane-bound proteins.
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.
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.
Based on the hg38 reference genome, paired-end reads are mapped by STAR aligner. The mapped reads are used for expression quantification without assembling transcripts by counting the number of reads that map to an exon by HTSeq that uses Refseq gene annotations. Then, to correct for systematic variability such as library fragment size, sequence composition bias, and read depth the raw counts are normalized as trimmed mean of M-values (TMM) through edgeR.
Published:
A simple RNA-Seq differential expression analysis using High Performance Computing (HPC).
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.
Based on the hg38 reference genome, paired-end reads are mapped by STAR aligner. The mapped reads are used for expression quantification without assembling transcripts by counting the number of reads that map to an exon by HTSeq that uses Refseq gene annotations. Then, to correct for systematic variability such as library fragment size, sequence composition bias, and read depth the raw counts are normalized as trimmed mean of M-values (TMM) through edgeR.
Published:
This workflow consists of taxonomic and functional profiling of shotgun metagenomics sequencing (MGS) reads using MetaPhlAn2 and HUMAnN2, respectively. To perform taxonomic (phyla, genera or species level) profiling of the MGS data, the MetaPhlAn2 pipeline was run on a high performance multicore cluster computing environment.
Published:
Copy number variations (CNVs) represent gain or loss of genomic regions. CNVs transmit from parents to offspring or arise de novo and play important role in neuro-psychiatric disorders and cancers.
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.
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.
Based on the hg38 reference genome, paired-end reads are mapped by STAR aligner. The mapped reads are used for expression quantification without assembling transcripts by counting the number of reads that map to an exon by HTSeq that uses Refseq gene annotations. Then, to correct for systematic variability such as library fragment size, sequence composition bias, and read depth the raw counts are normalized as trimmed mean of M-values (TMM) through edgeR.
Published:
The human complement activation takes place through one or more of the well-established pathways consisting of plasma and membrane-bound proteins.
Published:
Updated on September 13, 2021
Published:
Quantification of proteins using isobaric labeling (tandem mass tag or TMT) starts with the reduction of disulfide bonds in proteins with Dithiothreitol (DTT).
Published:
Updated on September 13, 2021
Published:
This workflow consists of taxonomic and functional profiling of shotgun metagenomics sequencing (MGS) reads using MetaPhlAn2 and HUMAnN2, respectively. To perform taxonomic (phyla, genera or species level) profiling of the MGS data, the MetaPhlAn2 pipeline was run on a high performance multicore cluster computing environment.
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.
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.
Published:
The human complement activation takes place through one or more of the well-established pathways consisting of plasma and membrane-bound proteins.
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.
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.
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.
Published:
This workflow consists of taxonomic and functional profiling of shotgun metagenomics sequencing (MGS) reads using MetaPhlAn2 and HUMAnN2, respectively. To perform taxonomic (phyla, genera or species level) profiling of the MGS data, the MetaPhlAn2 pipeline was run on a high performance multicore cluster computing environment.
Published:
Quantification of proteins using isobaric labeling (tandem mass tag or TMT) starts with the reduction of disulfide bonds in proteins with Dithiothreitol (DTT).
Published:
This workflow consists of taxonomic and functional profiling of shotgun metagenomics sequencing (MGS) reads using MetaPhlAn2 and HUMAnN2, respectively. To perform taxonomic (phyla, genera or species level) profiling of the MGS data, the MetaPhlAn2 pipeline was run on a high performance multicore cluster computing environment.