{"id":671,"date":"2020-05-20T13:14:08","date_gmt":"2020-05-20T13:14:08","guid":{"rendered":"https:\/\/apexbtic.icgeb.res.in\/btisnet\/?page_id=671"},"modified":"2020-08-05T12:00:15","modified_gmt":"2020-08-05T12:00:15","slug":"resources","status":"publish","type":"page","link":"https:\/\/apexbtic.icgeb.res.in\/btisnet\/resources\/","title":{"rendered":"List of Standalone Software developed by BTISNet staff"},"content":{"rendered":"\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
S.No.<\/th>\nPrincipal Investigator<\/th>\nEmail<\/th>\nSoftware<\/th>\nDescription<\/th>\nReference<\/th>\n<\/tr>\n
1.<\/td>\nDr. Santhosh J. Eapen<\/td>\nsjeapen@spices.res.in<\/td>\nRNAseqAnalysis<\/a><\/td>\n\n
\n
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.<\/span><\/div>\n<\/div>\n<\/td>\n
https:\/\/github.com\/DISC-IISR\/RNAseqAnalysis<\/a><\/td>\n<\/tr>\n
2.<\/td>\nDr. Santhosh J. Eapen<\/td>\nsjeapen@spices.res.in<\/td>\nRAPID<\/a><\/td>\nRAPiD is an add-on for identifying the unique bands by generating different colors (from the inputted gel data \u201c0\u201d or \u201c1\u201d 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.<\/td>\nhttp:\/\/14.139.189.27\/spicebioinfo\/tools\/rapid\/
\n<\/a><\/td>\n<\/tr>\n
3.<\/td>\nProf. Mukesh Kumar Gupta<\/td>\nmukeshkgupta@gmail.com<\/td>\nA graphical user interface (GUI) for bioinformatics workstation<\/a><\/td>\nCatholicon v3<\/td>\nhttps:\/\/www.dropbox.com\/s\/hcjdom81geua1qi\/Catholicon%20v3%20%28flash%20version%29.rar?dl=0
\n<\/a><\/td>\n<\/tr>\n
4.<\/td>\nProf. Mukesh Kumar Gupta<\/td>\nmukeshkgupta@gmail.com<\/td>\nA software for tracing stem cell niche and lineage<\/a><\/td>\nInigo Software Simulation-20200523T090311Z-001<\/td>\nhttps:\/\/drive.google.com\/drive\/folders\/1QvBkpLkcBakf8bTyZNg6mZ4FUZcXphIi
\n<\/a><\/td>\n<\/tr>\n
5.<\/td>\nM Krishna Mohan<\/td>\nkmohan@bisr.res.in<\/td>\nWhole Exome Sequencing Pipeline<\/a><\/td>\nA Bioinformatics Pipeline for Whole Exome Sequencing: Overview of the Processing and Steps from Raw Data to Downstream Analysis<\/td>\nhttps:\/\/bio-protocol.org\/bio101\/e2805<\/a><\/td>\n<\/tr>\n
6.<\/td>\nDr. Sumita Kachhwaha<\/td>\nkachhwahasumita@rediffmail.com<\/td>\nTravel to phylogeny<\/a><\/td>\nThis is an automated platform<\/td>\nhttps:\/\/github.com\/DBT-BIF\/Biosensor-Python<\/a><\/td>\n<\/tr>\n
7.<\/td>\nDr. Shandar Ahmad<\/td>\nshandar@jnu.ac.in<\/td>\nPLncPRO<\/a><\/td>\nPlant Long Non-Coding RNA Prediction by Random forests<\/td>\nhttp:\/\/ccbb.jnu.ac.in\/plncpro\/<\/a><\/td>\n<\/tr>\n
8.<\/td>\nDr. Shandar Ahmad<\/td>\nshandar@jnu.ac.in<\/td>\nORIS<\/a><\/td>\nOrigin search in genomics<\/td>\nhttp:\/\/ccbb.jnu.ac.in\/oris\/<\/a><\/td>\n<\/tr>\n
9.<\/td>\nDr. Shandar Ahmad<\/td>\nshandar@jnu.ac.in<\/td>\nDynaSeq<\/a><\/td>\nDynaSeq model DNA sequence specificities using MD-derived sequence-dependent conformational ensembles, instead of their static values.<\/td>\nhttp:\/\/dynaseq.sciwhylab.org<\/a><\/td>\n<\/tr>\n
10.<\/td>\nDr. Dineshram R<\/td>\ndinesh@nio.org<\/td>\nDatabase on Marine Prawns of India<\/a><\/td>\nDatabase on Marine Life of India Modue 1 Marine Prawns of India<\/td>\nhttp:\/\/www.niobioinformatics.in\/prawns\/Index.htm<\/a><\/td>\n<\/tr>\n
11.<\/td>\nDr. Dineshram R<\/td>\ndinesh@nio.org<\/td>\nMarien Crabs of India (Module 2)<\/a><\/td>\nUnder NIO’s Database on Marine Life of India a CDROM on Marine Crabss of India (Module 2) was developed<\/td>\nhttp:\/\/www.niobioinformatics.in\/crab\/index.html<\/a><\/td>\n<\/tr>\n
12.<\/td>\nDr. Dineshram R<\/td>\ndinesh@nio.org<\/td>\nMangroves of India<\/a><\/td>\nUnder the database NIO’s Database on Marine Life of India and CDROM on Mangroves of India Module 3 was developed and published<\/td>\nhttp:\/\/www.niobioinformatics.in\/mangroves\/index.htm<\/a><\/td>\n<\/tr>\n
13.<\/td>\nDr. Dineshram R<\/td>\ndinesh@nio.org<\/td>\nMarien Lignicolous Fungi<\/a><\/td>\nUnder the databae NIO’s Database on Marine Life of India “Marine Lignicolous Fungi (Modul4) was developed<\/td>\nhttp:\/\/www.niobioinformatics.in\/fungi\/index.htm<\/a><\/td>\n<\/tr>\n
14.<\/td>\nDr. Dineshram R<\/td>\ndinesh@nio.org<\/td>\nSeaweeds of Central West Coast of India<\/a><\/td>\nUnder the NIO’s database on Marine Life of India a CDROM on Seaweeds of Central West Coast of India (Module 5) was developed.<\/td>\nhttp:\/\/www.niobioinformatics.in\/seaweed\/index.htm<\/a><\/td>\n<\/tr>\n
15.<\/td>\nDr. Dinesh Gupta<\/td>\ndinesh@icgeb.res.in<\/td>\nGFF-Ex<\/a><\/td>\nThere 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.<\/td>\nhttp:\/\/bioinfo.icgeb.res.in\/gff<\/a><\/td>\n<\/tr>\n
16.<\/td>\nDr. Dinesh Gupta<\/td>\ndinesh@icgeb.res.in<\/td>\nAPA<\/a><\/td>\nAltered 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<\/td>\nhttp:\/\/bioinfo.icgeb.res.in\/APA<\/a><\/td>\n<\/tr>\n
17.<\/td>\nDr. Achuthsankar S. Nair<\/td>\nsankar.achuth@gmail.com<\/td>\nC-GREx<\/a><\/td>\nC-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.<\/td>\nhttps:\/\/sites.google.com\/site\/cgrexonline\/
\n<\/a><\/td>\n<\/tr>\n
18.<\/td>\nProf. Ragini Gothalwal<\/td>\nbarhuniv.btisnet@nic.in<\/td>\nMicrobial Genomics Tool V 1 (MGT)<\/a><\/td>\nMGT 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 –
\n1. 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.
\n2. User-friendly graphical interface
\n3. It provides application for calculation of codon frequency, RSCU, AT3, GC3, Nc Enc, nucleotide composition and percent values.
\n4. Result can be viewed in MS-Excel sheet.
\n5. MGT development was initiated with the future intention to provide multi-application software for bacterial genome analysis.<\/td>\n		https:\/\/sourceforge.net\/projects\/microbial-genomics-tools\/<\/a><\/td>\n<\/tr>\n
19.<\/td>\nProf. H.A.Nagarajaram<\/td>\nhansl@uohyd.ac.in<\/td>\nmaGUI<\/a><\/td>\nmaGUI<\/td>\nhttp:\/\/bif.uohyd.ac.in\/maGUI\/<\/a><\/td>\n<\/tr>\n<\/table>\n

 <\/p>\n","protected":false},"excerpt":{"rendered":"

S.No. Principal Investigator Email Software Description Reference 1. Dr. Santhosh J. Eapen sjeapen@spices.res.in RNAseqAnalysis The package RNAseqAnalysis does the complete […]<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"site-sidebar-layout":"default","site-content-layout":"","ast-site-content-layout":"","site-content-style":"default","site-sidebar-style":"default","ast-global-header-display":"","ast-banner-title-visibility":"","ast-main-header-display":"","ast-hfb-above-header-display":"","ast-hfb-below-header-display":"","ast-hfb-mobile-header-display":"","site-post-title":"","ast-breadcrumbs-content":"","ast-featured-img":"","footer-sml-layout":"","theme-transparent-header-meta":"","adv-header-id-meta":"","stick-header-meta":"","header-above-stick-meta":"","header-main-stick-meta":"","header-below-stick-meta":"","astra-migrate-meta-layouts":"default","ast-page-background-enabled":"default","ast-page-background-meta":{"desktop":{"background-color":"var(--ast-global-color-4)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-gradient":""},"tablet":{"background-color":"","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-gradient":""},"mobile":{"background-color":"","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-gradient":""}},"ast-content-background-meta":{"desktop":{"background-color":"var(--ast-global-color-5)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-gradient":""},"tablet":{"background-color":"var(--ast-global-color-5)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-gradient":""},"mobile":{"background-color":"var(--ast-global-color-5)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-gradient":""}}},"_links":{"self":[{"href":"https:\/\/apexbtic.icgeb.res.in\/btisnet\/wp-json\/wp\/v2\/pages\/671"}],"collection":[{"href":"https:\/\/apexbtic.icgeb.res.in\/btisnet\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/apexbtic.icgeb.res.in\/btisnet\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/apexbtic.icgeb.res.in\/btisnet\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/apexbtic.icgeb.res.in\/btisnet\/wp-json\/wp\/v2\/comments?post=671"}],"version-history":[{"count":96,"href":"https:\/\/apexbtic.icgeb.res.in\/btisnet\/wp-json\/wp\/v2\/pages\/671\/revisions"}],"predecessor-version":[{"id":1742,"href":"https:\/\/apexbtic.icgeb.res.in\/btisnet\/wp-json\/wp\/v2\/pages\/671\/revisions\/1742"}],"wp:attachment":[{"href":"https:\/\/apexbtic.icgeb.res.in\/btisnet\/wp-json\/wp\/v2\/media?parent=671"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}