1. Heatmaps: Exploring Patterns in High-Dimensional Data

Heatmaps are a go-to visualization for representing high-dimensional datasets, such as gene expression or metabolomics data. They use color gradients to display data intensity, making patterns and clusters easily detectable.

• Applications: Gene expression analysis, pathway enrichment, methylation studies.

• Tools: Seaborn (Python), ComplexHeatmap (R), Morpheus (web-based).

Tip: Add dendrograms to visualize clustering of rows and columns for hierarchical relationships.

2. Volcano Plots: Highlighting Differential Features

Volcano plots are indispensable for identifying significantly differentially expressed genes or proteins. They plot the log2 fold change against –log10(p-value), making it easy to spot statistically significant changes.

• Applications: RNA-seq, proteomics, and metabolomics.

• Tools: ggplot2 (R), EnhancedVolcano (R), Plotly (Python).

Tip: Use color to highlight significant features and label key genes or proteins.

3. PCA Plots: Reducing Complexity with Principal Component Analysis

Principal Component Analysis (PCA) plots are used to reduce dimensionality and uncover trends or clusters in data. They provide insights into sample variability and grouping.

• Applications: Transcriptomics, metabolomics, microbiome studies.

• Tools: scikit-learn + Matplotlib (Python), prcomp (R), ClustVis (web-based).

Tip: Annotate clusters with metadata to enhance interpretability.

4. Manhattan Plots: Genome-Wide Association Studies

Manhattan plots visualize p-values across the genome, making it easy to identify significant associations in genome-wide studies. They resemble city skylines, with the highest peaks indicating loci of interest.

• Applications: GWAS, QTL mapping.

• Tools: qqman (R), Matplotlib (Python).

Tip: Use alternating colors for chromosomes and highlight significant SNPs for clarity.

5. Circular Plots (Circos): Visualizing Genomic Relationships

Circular plots are ideal for visualizing relationships across the genome, such as structural variations, gene duplications, or synteny.

• Applications: Comparative genomics, structural variation studies.

• Tools: Circos (standalone), Rcircos (R), pyCircos (Python).

Tip: Keep the plot clean and avoid overcrowding to maintain readability.

6. Sankey Diagrams: Tracking Data Flows

Sankey diagrams visualize flows or relationships between categories, often used to track changes in gene expression or pathway enrichment across conditions.

• Applications: Pathway analysis, gene set enrichment analysis.

• Tools: Plotly (Python), networkD3 (R).

Tip: Use gradients or distinct colors to highlight key transitions.

7. Network Graphs: Mapping Interactions

Network graphs represent relationships between entities, such as protein-protein interactions or gene regulatory networks. Nodes represent entities, and edges represent relationships.

• Applications: Systems biology, interactomics.

• Tools: Cytoscape (standalone), igraph (R), NetworkX (Python).

Tip: Use edge thickness or node size to represent interaction strength or centrality.

8. Violin Plots: Visualizing Data Distribution

Violin plots combine a boxplot with a density plot, showing the distribution and variability of data.

• Applications: Single-cell RNA-seq, quantitative trait analysis.

• Tools: Seaborn (Python), ggplot2 (R).

Tip: Split violins by groups for side-by-side comparisons.

9. Time-Series Plots: Monitoring Changes Over Time

Time-series plots display changes in variables across time points, useful for tracking gene expression dynamics or metabolic fluxes.

• Applications: Time-course experiments, cell cycle studies.

• Tools: Matplotlib (Python), ggplot2 (R).

Tip: Smooth the data to highlight trends while avoiding overfitting.

10. Genome Tracks: Visualizing Genomic Features

Genome tracks display multiple layers of genomic data, such as gene annotations, sequencing coverage, and epigenetic marks.

• Applications: ChIP-seq, ATAC-seq, whole-genome sequencing.

• Tools: IGV (standalone), pyGenomeTracks (Python).

Tip: Stack related tracks for direct comparisons.

11. UpSet Plots: Visualizing Set Intersections

UpSet plots are a powerful alternative to Venn diagrams for visualizing intersections between multiple datasets.

• Applications: Overlap analysis for gene sets, pathways, or variants.

• Tools: UpSetR (R), ComplexUpset (Python).

Tip: Use bar plots to represent the size of each intersection for added clarity.

12. Ridge Plots: Comparing Distributions

Ridge plots visualize the distributions of multiple datasets, stacked for easy comparison.

• Applications: Transcriptomics, single-cell RNA-seq.

• Tools: ggridges (R), Matplotlib (Python).

Tip: Use transparency and consistent scaling for better readability.

13. Chord Diagrams: Visualizing Connections Between Groups

Chord diagrams illustrate relationships between categories, such as shared genes between pathways or overlaps in regulatory elements.

• Applications: Pathway overlap, synteny, co-expression networks.

• Tools: Circlize (R), Holoviews (Python).

Tip: Use distinct colors for each group to emphasize relationships.

14. Treemaps: Hierarchical Data Representation

Treemaps visualize hierarchical data as nested rectangles, with area proportional to data size.

• Applications: Ontology enrichment, pathway analysis.

• Tools: Treemapify (R), Plotly (Python).

Tip: Use colors to represent additional variables, like significance or enrichment scores.

15. T-SNE/UMAP Plots: Dimensionality Reduction for Clustering

T-SNE and UMAP plots are great for visualizing high-dimensional data in two dimensions while preserving local or global structure.

• Applications: Single-cell transcriptomics, clustering analyses.

• Tools: scikit-learn (Python), Seurat (R).

Tip: Combine with metadata annotations for better cluster interpretation.

Bringing It All Together

The choice of visualization can significantly impact the insights gained from bioinformatics data. By selecting plots tailored to your data type and analysis goals, you can effectively communicate your findings and make your research more impactful. Whether you’re a seasoned bioinformatician or a beginner, mastering these visualizations will elevate your analyses and presentations.

No of vacancies: 01

Pay scale:Rs. 15600 – 39100 + 6600/-

Essential Academic Qualifications / Experience : Good academic record as defined by the concerned university with at least 55% marks (or an equivalent grade in a point scale wherever grading system is followed) at the Master's Degree level in a relevant subject from an Indian University, or an equivalent degree from an accredited foreign university.

Besides fulfilling the above qualifications, the candidate must have cleared the National Eligibility Test (NET) conducted by the UGC, CSIR or similar test accredited by the UGC like SLET/ SET.

Notwithstanding anything contained in sub-clauses (a) and (b) to this Clause, candidates, who are, or have been awarded a Ph.D. Degree in accordance with the University Grants Commission (Minimum Standards and Procedure for Award of Ph.D. Degree) Regulations, 2009, shall be exempted from the requirement of the minimum eligibility condition of NET/SLET/SET for recruitment and appointment of Assistant Professor or equivalent positions in Universities/Colleges/Institutions.

NET/SLET/SET shall also not be required for such Masters Programmes in disciplines for which NET/SLET/SET is not conducted.

Apply online: http://www.psc.cg.gov.in/htm/OA_ME2014.html

Last Date for Online Registration: 22/05/2014

For more details: http://www.psc.cg.gov.in/pdf/Advertisement/ADV_ME2014.pdf

Installation

General Usage Guide

Data Preprocessing Guide

Specific Tool Guides:

• BBDuk
• BBMap
• BBMask
• BBMerge
• BBNorm
• CalcUniqueness
• Clumpify
• Dedupe
• Reformat
• Repair
• Seal
• Split Nextera
• Statistics
• Tadpole
• Taxonomy

https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/

Address of the bookmark: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/

More at http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000369

Address of the bookmark: http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000369

More detail http://perlmaven.com/

ICRISAT seeks applications from Indian nationals Visiting Scientist-Computational Genomics (2 positions), to be part of a team of Centre of Excellence in Genomics (CEG), (www.icrisat.org/ceg) to work on legume genomics projects. The positions will be based at ICRISAT’s Headquarters in Patancheru, Hyderabad, India.

ICRISAT is a non-profit, non-political organization that conducts agricultural research for development in Asia and sub-Saharan Africa with a wide array of partners throughout the world. Covering 6.5 million square kilometers of land in 55 countries, the semi-arid tropics is home to over 2 billion people, with 650 million of these are the poorest of the poor. ICRISAT and its partners help empower those living in the semi-arid tropics, especially smallholder farmers, to overcome poverty, hunger, malnutrition and a degraded environment through more efficient and profitable agriculture. ICRISAT is headquartered in Greater Hyderabad, Andhra Pradesh, India and belongs to the Consortium of Centers supported by the Consultative Group on International Agricultural Research (CGIAR).

The Job: Responsibilities for these positions include:

Analyzing and handling large-scale next generation sequencing DNA and RNA data
Data mining and development of pipelines and troubleshooting
Genome diversity analysis such as SNPs, Indels, Structural Variations, population structure
Genome wide association study (GWAS) related analysis- LD analysis, hapmap and trait mapping
Expression analysis based on RNA-Seq data, annotation, gene ontology and metabolic pathway analysis
Epigenome analysis, small RNA identification
Gene family analysis, sequence level protein analysis, orthology/paralogy and molecular modelling
Compiling and analysis of results, writing reports and research papers

The Person: Ph.D. or MSc/MTech/PGDCA with two years research experience in Biotechnology, Computational biology, Agricultural/ Plant Biotechnology, Genetics, Molecular Biology or related discipline. Good knowledge of programming/scripting in at least two of following languages: Perl, C, C++, R, Shell Scripting and Python is plus.

How to apply: Please apply latest by 20 July 2014. The application should include the name of the position applied for, a letter of motivation, a full Curriculum Vita (CV), and the names and contact information of three references that are knowledgeable of the candidate’s professional qualifications and work experience. Technical details and more information about these positions can be obtained from R.K.VARSHNEY@CGIAR.ORG. All applications will be acknowledged, however only short listed candidates will be contacted.

Apply here https://recruit.zoho.com/ats/Portal.na?digest=T642sgLYWZOStExJ77cPrcM*sIMGZETWw4yPxngbmHA-

Supported Perl Versions

Threaded Perl with a shared libperl  5.8, 5.10, 5.12, 5.14, 5.16

Supported Operating Systems

    MS Windows XP and later 32 and 64 bit.

    Linux 32 and 64 bit - minimum glibc 2.5, GTK+ 2.10, libstdc++6.

    Linux 32 bit  RHEL 3 and 4.

    Mac OSX 10.4 and 10.5 - ppc and i386.

    Mac OSX 10.6, 10.7, 10.8  - i386 and x86_64 ( 64 bit for Perl 5.16 only ).

Address of the bookmark: http://www.cavapackager.com/

Address of the bookmark: http://www.programmingr.com/category/stype/r-job-listings/