GenFam: gene family‐based classification and functional enrichment analysis
Posts by Category
- High-throughput sequence analysis 9
- Genomic visualization 5
- Gene expression 4
- Variant analysis 3
- Statistical bioinformatics 3
- Unsupervised machine learning 2
- Clustering 2
- Exploratory data analysis 2
- Dimensionality reduction 2
- Genotyping 2
- Biostatistics 2
- Python 2
- Supervised machine learning 2
- Sequence quality control analysis 1
- Biological data handling 1
- Variant Annotation 1
- Functional enrichment 1
- Plant Genomics 1
- Machine learning 1
- Statistics 1
- Classification 1
High-throughput sequence analysis
Bioinformatics file readers and processing (FASTA, FASTQ, and VCF)
Bioinformatics file readers We will discuss how to read and process common bioinformatics files We will use bioinfokit v0.8.4 or later Check bioinfoki...
Convert GFF3 to GTF file format
What is GFF3 file format? GFF3 (Generic Feature Format Version 3) file format represents the genomic features in a simple text-based tab-delimited file ...
Manhattan plot
What is Manhattan plot? Manhattan plot used to visualize the association of SNPs with given trait or disease as statistical significance in terms of P-va...
Sequencing coverage and breadth of coverage
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Genomic visualization
Convert GFF3 to GTF file format
What is GFF3 file format? GFF3 (Generic Feature Format Version 3) file format represents the genomic features in a simple text-based tab-delimited file ...
Manhattan plot
What is Manhattan plot? Manhattan plot used to visualize the association of SNPs with given trait or disease as statistical significance in terms of P-va...
Heatmap in Python
What is heatmap? Continuous colormap where each color represents a specific set of values Great way to visualize and identify statistically significant ...
Gene expression
Convert GFF3 to GTF file format
What is GFF3 file format? GFF3 (Generic Feature Format Version 3) file format represents the genomic features in a simple text-based tab-delimited file ...
Heatmap in Python
What is heatmap? Continuous colormap where each color represents a specific set of values Great way to visualize and identify statistically significant ...
Variant analysis
Annotation of genetic variants (SNPs/InDels) in VCF file
The Variant Call Format (VCF) file produced by variant calling software (e.g. GATK, FreeBayes, BCFtools) contains the information for polymorphic loci pre...
Manhattan plot
What is Manhattan plot? Manhattan plot used to visualize the association of SNPs with given trait or disease as statistical significance in terms of P-va...
Statistical bioinformatics
t-SNE in Python
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Unsupervised machine learning
t-SNE in Python
Check updated page here
Clustering
Heatmap in Python
What is heatmap? Continuous colormap where each color represents a specific set of values Great way to visualize and identify statistically significant ...
Exploratory data analysis
t-SNE in Python
Check updated page here
Dimensionality reduction
t-SNE in Python
Check updated page here
Genotyping
Annotation of genetic variants (SNPs/InDels) in VCF file
The Variant Call Format (VCF) file produced by variant calling software (e.g. GATK, FreeBayes, BCFtools) contains the information for polymorphic loci pre...
Biostatistics
Chi-square test in Python
Check updated page here
t-test in Python
Check updated page here
Python
Back to top ↑Supervised machine learning
Multiple linear regression (MLR)
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Sequence quality control analysis
Back to top ↑Biological data handling
Bioinformatics file readers and processing (FASTA, FASTQ, and VCF)
Bioinformatics file readers We will discuss how to read and process common bioinformatics files We will use bioinfokit v0.8.4 or later Check bioinfoki...
Variant Annotation
Annotation of genetic variants (SNPs/InDels) in VCF file
The Variant Call Format (VCF) file produced by variant calling software (e.g. GATK, FreeBayes, BCFtools) contains the information for polymorphic loci pre...