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afplot

Plot allele frequencies in VCF files

agfusion

Python package to annotate and visualize gene fusions.

allelefrequencyapp

Allele frequency filter app

altanalyze

AltAnalyze is a multi-functional and easy-to-use software package for automated single-cell and bulk gene and splicing analyses. Easy-to-use precompiled graphical user-interface versions available from our website.

anndata

Annotated data.

appraise

A Bayesian framework for the analysis and interpretation of rare genetic variants

bammsc

bermuda

BERMUDA (Batch Effect ReMoval Using Deep Autoencoders) is a novel transfer-learning-based method for batch correction in scRNA-seq data.

bicg_2018

Bioinformatics of Cancer Genomics 2018 workshop

bioinformatics

bionexr

an R package for integrative network-based analysis of gene somatic mutation and gene expression data to identify cancer drivers

biotoolsregistry

biotoolsregistry : discovery portal for bioinformatics

biscuit_singlecell_imm_icml_2016

R Codebase for BISCUIT: Infinite Mixture Model to cluster and impute single cells.

bpsomatic

Bioinformatic pipeline for finding somatic variants from NGS-data. This pipeline is in progress and will be improved regularly. The aim is to make a simple to use pipeline that can produce high-quality variant calls.

breakid

BreakID: genomics breakpoints identification to detect gene fusion events using discordant pairs and split read

busseq-0.99.0

Batch Effect Correction with Unknown Subtypes for scRNA-seq Data

cancerdiscover

Open-source software pipeline for cancer classification from high-throughput data using machine learning.

cancereffectsizer

cancereffectsizeR: an R package to measure the cancer effect size of somatic mutations

cancerpipeline

Scripts for Bioinformatics Analysis of Cancer.

cbioportal

cBioPortal for Cancer Genomics

ccinx

Build predicted cell-cell interaction networks from single-cell data.

cell_blast

A BLAST-like Toolkit for large-scale scRNA-seq Data Querying and Annotation.

cerebro

Visualize scRNA-seq results.

cerebroapp

R package containing the Cerebro application.

cerebroprepare

R package containing functions to prepare single-cell transcriptomics data saved in a Seurat object for visualization in Cerebro, as well as perform few analytical procedures.

chimpipe

ChimPipe: Accurate detection of fusion genes and transcription-induced chimeras from RNA-seq data

chromosomematrices

Scripts for intra-chromosomal analysis of gene expression in breast cancer

cidr

Clustering through Imputation and Dimensionality Reduction

clinker

Gene Fusion Visualiser

clonevol

Inferring and visualizing clonal evolution in multi-sample cancer sequencing