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icallsv

A Framework to call Structural Variants from NGS based datasets

icc

R package to assist in the estimation of the Intraclass Correlation Coefficient (ICC).

igraph

Library for the analysis of networks

immunespacer

A thin wrapper around Rlabkey to access the ImmuneSpace database from R

indels

infercnv

Inferring CNV from Single-Cell RNA-Seq

innovation-impact-pipeline

Framework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay

install-tl-ubuntu

Install script for TeX Live on Ubuntu

intermediate

small R utility for mediation analysis

intro_to_gwas

An introductory workshop to GWAS analysis using PLINK and R

introduction_to_googlevis

Introduction to googleVis

inverted_repeats

Detecting and clipping artifactual inverted repeats in Illumina reads

ipanda

insilico Pathway Activation Network Decomposition Analysis (iPANDA) package. Owned by Insilico Medicine Inc. iPANDA is a pathway analysis method that aids interpretation of large-scale gene expression data. The method introduced here includes coexpression analysis and gene importance estimation to robustly identify relevant pathways and biomarkers for patient stratification.

irls

C++ implementation of IRLS algorithm for generalized linear model

isa-api

ISA tools API

isingfit

This network estimation procedure combines l1-regularized logistic regression with model selection based on the Extended Bayesian Information Criterion to identify relevant symptom-symptom relationships. These relationships define connections in a network.

isop

Isoform-level expression patterns in single-cell RNA-sequencing data

isotopemodels

prediction and description of isotopomer intensity distribution

itraqtools

Some R functions for analyzing iTRAQ data

jaffa

JAFFA is a multi-step pipeline that takes either raw RNA-Seq reads, or pre-assembled transcripts, then searches for gene fusions

jamm

JAMM Peak Finder for Sequencing Datasets

jfuzzylogic

The most complete fuzzy logic library in Java. The de-facto standard for research and industrial applications.

json-c

https://github.com/json-c/json-c is the official code repository for json-c. See the wiki for release tarballs for download.

kallisto

Near-optimal RNA-Seq quantification

kallisto-align

kallisto-sleuth-workshop-2016

materials and website for the 2016 kallisto sleuth workshop

kat

keemei

Validate tabular bioinformatics file formats in Google Sheets

kernel_regression_matlab

A tiny functions collection for Matlab and Octave to do some machine learning research on multidimensional datasets.

kggseq