reemasingh Goto Github PK

dictostelium_differential_expression_experiment

Identify Differential Expressed Genes in DgcA null mutant and Knock-out samples in Dictyostelium discoideum. The same workflow has been used for the differential expression analysis of Polysphondylium pallidum.

drreemasingh

gen2epi

A pipeline that assembles short reads into full scaffolds and automatically assigns molecular epidemiological and AMR information to the assembled genomes.

gen2epigui

Graphical User Interface (GUI) for the Gen2Epi computational pipeline named Gen2EpiGUI. Gen2Epi facilitates an understandable analysis of N. gonorrhoeae WGS data for users with limited bioinformatics skills.

htda

A generic platform for the analysis of high throughput transcriptomics, proteomics, and metabolomics data.

huanan-environmental

transcriptomics-assembly

De-novo Transcriptomics Assembly workflow for four Dictyostelium species (e.g.- Dictyostelium discoideum, Polysphondylium pallidum, Dictyostelium Lacteum and Dictyostelium Fasciculatum). This is the standard assembly workflow that should ideally work on any organism.Before normalizing first concatenate all RNAseq data across all samples into a single set of inputs to generate a single reference transcriptomics assembly. Combine all left reads in one file and all right reads in another file. In order to reduce the number, raw reads were normalized using in silico digital normalization implemented in trinity at 50X coverage. The reads were assembled with Trinity using kmer parameter of 25.