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anamir

An integrated analysis R package of miRNA and mRNA profiiling

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.

cnape

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

debks

a tool to detect differentially expressed circular RNA

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

dge_workshop

interest

IntEREst: Intron Exon Retention Estimator

intro-to-chipseq

Intro to ChIPseq using HPC

isotope

ISOform-guided prediction of epiTOPEs in cancer

methylation_analysis

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

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.

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)

nanostring_normalization_meta

nanostringnctools

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

nanostringnormalization

phlyip-distance-to-mega-distance

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

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 tutorial is created for educational purpose

scrna-seq

scrna-seq_online

somatic-shortv

training-material

A collection of Galaxy-related training material