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10xpilot_snrnaseq-human

10x snRNA-seq study on 5 postmortem human brain regions across the reward circuitry: NAc, AMY, sACC, DLPFC, and HPC

16s-vsearch-nf

vsearch based 16S targeted metagenomics pipeline

2020_scworkshop

Code and data repository for the 2020 physalia course on single cell RNA sequencing.

2020_wilk_covid

Reproducibility repository accompanying Wilk, Rustagi, Zhao, et al. "A single-cell atlas of the peripheral immune response to severe COVID-19"

3d-plotting-in-seurat-3.0.0

This repository contains R code, with which you can create 3D tSNE plots of Seurat analyzed scRNAseq data

3mcorserver

3MCor: an integrative web server for metabolome-microbiome-metadata correlation analysis

abismal

Abismal is a mapper of FASTQ bisulfite-converted short reads (between 50 and 1000 bases) to a FASTA reference genome.

act_paper

Scripts used for the ACT paper

actinn

aging-mice-snrnaseq

R script(s) for analysing aging mice brain snRNAseq data.

aims

AIMS bioconductor package

aluscancnv2

AluScanCNV2 is an R package that integrates the cross-platform CNV detection and tumor prediction function on the basis of AluScanCNV software developed in the early stage.

ampliconarchitect

AmpliconArchitect (AA) is a tool to identify one or more connected genomic regions which have simultaneous copy number amplification and elucidates the architecture of the amplicon. In the current version, AA takes as input next generation sequencing reads (paired-end Illumina reads) mapped to the hg19/GRCh37 reference sequence and one or more regions of interest. Please "watch" this repository for improvements in runtime, accuracy and annotations for GRCh38 human reference genome coming up soon.

ancestry_pipeline

Provides helper scripts for inferring local ancestry, performing ancestry-specific PCA, etc

angular-bubbletree

Angular bubble tree chart using d3

annotatr

Package Homepage: http://bioconductor.org/packages/devel/bioc/html/annotatr.html Bug Reports: https://support.bioconductor.org/p/new/post/?tag_val=annotatr.

apec

Single cell epigenomic clustering based on accessibility pattern

apl

R package for computing Association Plots

aracne-ap

Network Reverse Engineering through AP inference of Mutual Information

arriba

Fast and accurate gene fusion detection from RNA-Seq data

atacannor

An accurate and robust cross-modality cell type annotation method for scATAC-seq data

autooncotator

Python programs for automatically annotate vcf (variant call) file with Oncotator by selenium webdriver

awesome-single-cell

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

banovichlab

Public code repository for the Banovich Lab at the Translational Genomics Research Institute (TGen).

bazam

A read extraction and realignment tool for next generation sequencing data

bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis

bcbio_validations

Validation runs using bcbio: germline, somatic, structural variant calling and RNA-seq analyses

bingleseq

BingleSeq - A user-friendly R package for Bulk and Single-cell RNA-Seq data analyses

bio-playground

miscellaneous scripts for bioinformatics/genomics that dont merit their own repo.

biocintegrativecancervis