2014

Official content for the Fall 2014 Harvard CS109 Data Science course

3dbarplot

A 3D barplot script for R. Can encode variables using both height and depth of columns.

adv-r

Advanced R programming: a book

affylumcna

Copy Number Alterations: Preprocessing, integration, and analysis of Affymetrix and Illumina data

al3n70rn

allenbrainpy

Python package to analyze Allen Humap Brain genes expression

altre

ALTered Regulatory Elements

annotables

Provides tables for annotating Ensembl Gene IDs.

annotatr

Annotation of Genomic Regions to Genomic Annotations

antigen.garnish

Ensemble neoepitope prediction from DNA variants in R.

arkas

This is the kallisto package

ascat

ASCAT copy number R package

ascatngs

Somatic copy number analysis using paired end sequencing

athena

Computational Framework to Analyse Spatial Heterogeneity in Visum, IMC or MIBI data sets

awesome-clonality

A curated list of awesome clonality and tumor heterogeneity resources

awesome-r

A curated list of awesome R frameworks, packages and software.

awesome-single-cell

List of software packages for single-cell data analysis, including RNA-seq, ATAC-seq, etc.

backspin

Biclustering algorithm

ballgown

isoform-level differential expression analysis in R

bammetrics

Tool to generate bam statistics and pdf/html reports.

bioawk

BWK awk modified for biological data

bios201

brainbrowser

Web-based visualization tools for neurological data.

chip-seq_preprocess

A preprocessing pipeline for ChIP-seq, including alignment, quality control, and visualization.

chorddiag

R interface to D3 chord diagrams

clinker

Gene Fusion Visualiser

clonal_analysis

Analysis Pipeline for Dissecting the Clonal Origins of Childhood Acute Lymphoblastic Leukemia By Single-Cell Genomics

clonevol

Inferring and visualizing clonal evolution in multi-sample cancer sequencing

close

Cna and LOh analysis with SEquencing data

clustering_on_transcript_compatibility_counts

Clustering cells from single cell RNA seq assays