amarinderthind

anamiR

An integrated analysis R package of miRNA and mRNA profiiling

CancerGenomicsCourse_EMBL-EBI

CaSpER

CGRphylo

CGR package for phylogeny. Pipeline compare multiple whole genome sequences using alignment free approach Chaos Game Representation (CGR). CRG core function creates the frequencies object for each sequence which can be used to calculate distances among sequences.

decontaminer

DecontaMiner is a tool designed and developed to investigate the presence of contaminating sequences in unmapped NGS data. It can suggest the presence of contaminating organisms in sequenced samples, that might derive either from laboratory contamination or from their biological source, and in both cases can be considered as worthy of further investigation and experimental validation. The novelty of DecontaMiner is mainly represented by its easy integration with the standard procedures of NGS data analysis, while providing a complete, reliable, and automatic pipeline. https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2684-x

EGFR-ap

EGFR-App

Intro-to-ChIPseq

Intro to ChIPseq using HPC

mutation_load_comparison_plot

This plot is useful for the comparison of mutational load across the cancer types, with input data in 2 coulmns i.e cancer types and mutatonal load for each samples in specificed cancer type.

RankerGUI

R script used for the preparation of the initial input file, i.e. merging of various studies by logFC (LogFC),

RNA-seq-tutorial-for-gene-differential-expression-analysis

This RNAseq data analysis tutorial is created for educational purpose

amarinderthind/RNA-seq-tutorial-for-gene-differential-expression-analysis

This RNAseq data analysis tutorial is created for educational purpose

amarinderthind/decontaminer

DecontaMiner is a tool designed and developed to investigate the presence of contaminating sequences in unmapped NGS data. It can suggest the presence of contaminating organisms in sequenced samples, that might derive either from laboratory contamination or from their biological source, and in both cases can be considered as worthy of further investigation and experimental validation. The novelty of DecontaMiner is mainly represented by its easy integration with the standard procedures of NGS data analysis, while providing a complete, reliable, and automatic pipeline. https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2684-x

amarinderthind/CGRphylo

CGR package for phylogeny. Pipeline compare multiple whole genome sequences using alignment free approach Chaos Game Representation (CGR). CRG core function creates the frequencies object for each sequence which can be used to calculate distances among sequences.

amarinderthind/Intro-to-ChIPseq

Intro to ChIPseq using HPC

amarinderthind/anamiR

An integrated analysis R package of miRNA and mRNA profiiling

amarinderthind/CancerGenomicsCourse_EMBL-EBI

amarinderthind/CaSpER

amarinderthind/CNAPE

[Source] CNAPE: A Software for Copy Number Alteration Prediction from Gene Expression in Human Cancers

amarinderthind/DEBKS

a tool to detect differentially expressed circular RNA

amarinderthind/DGE_workshop

amarinderthind/EGFR-ap

EGFR-App

amarinderthind/mutation_load_comparison_plot

This plot is useful for the comparison of mutational load across the cancer types, with input data in 2 coulmns i.e cancer types and mutatonal load for each samples in specificed cancer type.

amarinderthind/RankerGUI

R script used for the preparation of the initial input file, i.e. merging of various studies by logFC (LogFC),

amarinderthind/IntEREst

IntEREst: Intron Exon Retention Estimator

amarinderthind/ISOTOPE

ISOform-guided prediction of epiTOPEs in cancer

amarinderthind/Methylation_Analysis

Comprehensive tutorial for differential methylation analysis, differential variability analysis and integrative analysis

amarinderthind/NanoNormIter

Pre-processing of NanoString normalization data, as described in "An approach for normalization and quality control for NanoString RNA expression data" (Bhattacharya and Hamilton et al, 2020)

amarinderthind/NanoStringNCTools

Tools for NanoString Technologies nCounter Technology for reading RCC files into an ExpressionSet derived object, QC and normalization.

amarinderthind/NanostringNormalization

amarinderthind/phlyip-distance-to-Mega-distance

R script for conversion of phylip distance matrix to Mega distance matrix

amarinderthind/scRNA-seq

amarinderthind/scRNA-seq_online

amarinderthind/SeuratExtend

amarinderthind/Somatic-ShortV

amarinderthind/training-material

A collection of Galaxy-related training material