| S.No. | Principal Investigator | Software | Description | Reference | |
|---|---|---|---|---|---|
| 1. | Dr. Santhosh J. Eapen | sjeapen@spices.res.in | RNAseqAnalysis |
The package RNAseqAnalysis does the complete analysis of RNA seq data starting from raw reads. It provides the user with different functions like generation of QC report, filtering, assembly and GO-term annotation, differential expression analysis and heatmap generation, and Alternative splicing-site prediction.
|
https://github.com/DISC-IISR/RNAseqAnalysis |
| 2. | Dr. Santhosh J. Eapen | sjeapen@spices.res.in | RAPID | RAPiD is an add-on for identifying the unique bands by generating different colors (from the inputted gel data “0” or “1” for the absence or presence respectively) in a Microsoft Excel format directly from the Excel sheet. The resulting color bands can be clustered and analyzed further. RAPiD is an Excel Basic macro and can, therefore, be integrated directly into your installation of Excel, eliminating the need for an external program to analyze your gel bands. | http://14.139.189.27/spicebioinfo/tools/rapid/ |
| 3. | Prof. Mukesh Kumar Gupta | mukeshkgupta@gmail.com | A graphical user interface (GUI) for bioinformatics workstation | Catholicon v3 | https://www.dropbox.com/s/hcjdom81geua1qi/Catholicon%20v3%20%28flash%20version%29.rar?dl=0 |
| 4. | Prof. Mukesh Kumar Gupta | mukeshkgupta@gmail.com | A software for tracing stem cell niche and lineage | Inigo Software Simulation-20200523T090311Z-001 | https://drive.google.com/drive/folders/1QvBkpLkcBakf8bTyZNg6mZ4FUZcXphIi |
| 5. | M Krishna Mohan | kmohan@bisr.res.in | Whole Exome Sequencing Pipeline | A Bioinformatics Pipeline for Whole Exome Sequencing: Overview of the Processing and Steps from Raw Data to Downstream Analysis | https://bio-protocol.org/bio101/e2805 |
| 6. | Dr. Sumita Kachhwaha | kachhwahasumita@rediffmail.com | Travel to phylogeny | This is an automated platform | https://github.com/DBT-BIF/Biosensor-Python |
| 7. | Dr. Shandar Ahmad | shandar@jnu.ac.in | PLncPRO | Plant Long Non-Coding RNA Prediction by Random forests | http://ccbb.jnu.ac.in/plncpro/ |
| 8. | Dr. Shandar Ahmad | shandar@jnu.ac.in | ORIS | Origin search in genomics | http://ccbb.jnu.ac.in/oris/ |
| 9. | Dr. Shandar Ahmad | shandar@jnu.ac.in | DynaSeq | DynaSeq model DNA sequence specificities using MD-derived sequence-dependent conformational ensembles, instead of their static values. | http://dynaseq.sciwhylab.org |
| 10. | Dr. Dineshram R | dinesh@nio.org | Database on Marine Prawns of India | Database on Marine Life of India Modue 1 Marine Prawns of India | http://www.niobioinformatics.in/prawns/Index.htm |
| 11. | Dr. Dineshram R | dinesh@nio.org | Marien Crabs of India (Module 2) | Under NIO’s Database on Marine Life of India a CDROM on Marine Crabss of India (Module 2) was developed | http://www.niobioinformatics.in/crab/index.html |
| 12. | Dr. Dineshram R | dinesh@nio.org | Mangroves of India | Under the database NIO’s Database on Marine Life of India and CDROM on Mangroves of India Module 3 was developed and published | http://www.niobioinformatics.in/mangroves/index.htm |
| 13. | Dr. Dineshram R | dinesh@nio.org | Marien Lignicolous Fungi | Under the databae NIO’s Database on Marine Life of India “Marine Lignicolous Fungi (Modul4) was developed | http://www.niobioinformatics.in/fungi/index.htm |
| 14. | Dr. Dineshram R | dinesh@nio.org | Seaweeds of Central West Coast of India | Under the NIO’s database on Marine Life of India a CDROM on Seaweeds of Central West Coast of India (Module 5) was developed. | http://www.niobioinformatics.in/seaweed/index.htm |
| 15. | Dr. Dinesh Gupta | dinesh@icgeb.res.in | GFF-Ex | There are several ways of representing genomic features for whole genome sequences emerging from annotation projects. Of these, the GFF (Generic/General/ Feature Format) has emerged as a widely accepted, portable and successfully used flat file format for storing genome annotations. With an increasing interest in genome annotation projects, the need for reference annotations at coordinate and sequence level in raw formats has immensely increased the use of GFF files. GFF-Ex, a Genome Feature extraction package extracts Gene, Exon, Intron, Upstream Region of Gene (Promoters), Intergenic and CDS/cDNA sequences by just tweeting in the Genome Feature File (gff) along with the corresponding genome/chromosome sequence. GFF-Ex. is a fusion of shell and Perl, developed for platforms supporting UNIX based file system. | http://bioinfo.icgeb.res.in/gff |
| 16. | Dr. Dinesh Gupta | dinesh@icgeb.res.in | APA | Altered Pathway Analyzer (APA) is a cross-platform and standalone tool for analyzing gene expression datasets to highlight significantly rewired pathways across case-vs-control conditions. The Tool is designed to analyze human gene expression datasets (with Entrez ID); however, the analysis can be performed on gene expression datasets of other species by using appropriate flags and input files. APA algorithm is a unique prioritization algorithm that also uses the gene-regulatory networks to identify transcriptionally dysregulated pathways. It, thus, uses altered Transcription Factor (TF) and Target Gene (TG) relationship for prioritizing gene circuit rewired pathways. For Human datasets, it requires Gene expression matrices (RNAseq read count or Normalized gene expression values) with genes in Entrez ID format. For other species, please refer the manual | http://bioinfo.icgeb.res.in/APA |
| 17. | Dr. Achuthsankar S. Nair | sankar.achuth@gmail.com | C-GREx | C-GREx is a handy tool for those who are in sequence visualization and analysis of patterns in biological sequences. C-GREx packs a wide variety of exploration facilities using Chaos Game Representation in DNA, RNA and amino acid sequences. | https://sites.google.com/site/cgrexonline/ |
| 18. | Prof. Ragini Gothalwal | barhuniv.btisnet@nic.in | Microbial Genomics Tool V 1 (MGT) | MGT V1 was developed by Mr. Rajendra Verma (Project students) and Dr. Kishor Shende (Information Officer), at Bioinformatics Center, barkatullah University. This software is attributed as – 1. Microbial Genomic Tool (MGT 1.0), the first version is developed for In-silico research bacteria genomic study and useful for the Students and research scholars working in the field of Microbial Genomics. 2. User-friendly graphical interface 3. It provides application for calculation of codon frequency, RSCU, AT3, GC3, Nc Enc, nucleotide composition and percent values. 4. Result can be viewed in MS-Excel sheet. 5. MGT development was initiated with the future intention to provide multi-application software for bacterial genome analysis. |
https://sourceforge.net/projects/microbial-genomics-tools/ |
| 19. | Prof. H.A.Nagarajaram | hansl@uohyd.ac.in | maGUI | maGUI | http://bif.uohyd.ac.in/maGUI/ |