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adapterrmandqc

How to remove the adaptor sequence and FastQC

bashscriptsforbeginners

This repository will collect all my bash scripts for future use.

clinicalexomesequencing

In this project, I analysed clinical exome sequencing data from 16 human samples using Illumina DRAGEN Bio-IT Platform.

deseqanddeseq2

fpkm

This repository contains the code for FPKM value calculation.

mirna_analysis

mosquitogenomeanalysis

motiffun

An R package for searching user defined motif with functional annotation features

picard

A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

python_mine

r_mine

rna-seq-variant-calling

This code will use for variant calling of RNASeq data set.

rnaseqanddiffexp

RNASeq Pipeline And Differential Expression Analysis.

sigfeature

sigFeature: sigFeature is an R package which is able to find out the significant features using support vector machine recursive feature elimination method (SVM-RFE) (Guyon, I., et al. 2002) and t-statistic. Feature selection is an important part dealing with machine learning technology. SVM-RFE is recognized as one of the most effective filtering methods, which is based on a greedy algorithm that only finds the best possible combination for classification without considering the differentially significant features between the classes. To overcome this limitation of SVM-RFE, the proposed approach is tuned to find differentially significant features along with notable classification accuracy. This package is able to enumerate the feature selection of any two-dimensional (for binary classification) data such as a micro array etc. This vignette explains the use of the package in a publicly available micro array data set.

submer-central-limit-theorem

toy

tpm_using_dragrn

upsetr

An R implementation of the UpSet set visualization technique published by Lex, Gehlenborg, et al..

variantcaller

This pipeline will show you how to make a variant call step by step using different publickly available tools.