Rory Kirchner

Login: roryk

Company: Harvard School of Public Health

Location: Boston, Massachusetts

Bio: neuroscientist and programmer

Blog:

Blog:

Repositories

adam

A genomics processing engine and specialized file format built using Apache Avro, Apache Spark and Parquet. Apache 2 licensed.

AssotesteR

R package AssotesteR

awesome-single-cell

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

az_test

null

basejump

Base functions for bioinformatics and R package development.

bcbioBase

Base functions and generics for bcbio R packages.

bcbio-conda

conda recipes for bcbio python code and dependencies

bcbio-nextgen

Best-practice pipelines for fully automated high throughput sequencing analysis

bcbio-nextgen-test-data

Unit test data for bcbio-nextgen

bcbio.rnaseq

Mostly deprecated in favor of : https://github.com/hbc/bcbioRNASeq. Quality control, differential gene/transcript expression and pathway analysis for bcbio RNA-seq runs

bcbioRNASeq

Quality control and differential expression for bcbio RNA-seq experiments.

bcbioSinglecell

Utility functions for analysis of bcbio-nextgen single-cell RNA-seq data.

bcbio-test-data

null

bcbio.variation

Toolkit to analyze genomic variation data, built on the GATK with Clojure

bcbio.variation.recall

Parallel merging, squaring off and ensemble calling for genomic variants

bioconda-recipes

Conda recipes for the bioconda channel.

BioD

Bioinformatics library in D. (utils for working with SAM, BAM, SFF formats)

bipy

DEPRECATED Lightweight bioinformatics pipeline tools using iPython

breakseq2

BreakSeq2: Ultrafast and accurate nucleotide-resolution analysis of structural variants

brew-ds

Common Data Science set up for Mac ??

chanjo

Chanjo provides a better way to analyze coverage data in clinical sequencing.

chipseq-greylist

Python implementation of the GreyListChIP Bioconductor package

chowda

Python module for analysis of CLAMS (comprehensive lab animal monitoring system) data

ChromosomeMappings

This repository contains chromosome/contig name mappings between UCSC <-> Ensembl <-> Gencode for a variety of genomes.

clojupyter

a Jupyter kernel for Clojure

cnvkit

Copy number variant detection from targeted DNA sequencing

common-workflow-language

Repository for CWL Specifications. Use https://www.biostars.org/t/cwl/ for support.

compcodeR

null

conda-smithy

The tool for managing conda-forge feedstocks.

curl-feedstock

A conda-smithy repository for curl.

datasets

My datasets - Original data or Aggregated / cleaned / restructured existing datasets. Released here under Creative Commons B

deepvariant

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

DEGreport

Create a cromphensive report of DEG list coming from any analysis of RNAseq data

Delicious

Source code to Delicious bookmarking site, pull requests welcome

DEXSeq

Fork of DEXSeq, this is not the official DEXseq. For that go here: http://bioconductor.org/packages/release/bioc/html/DEXSeq.html

dge-vis

null

disambiguate

Disambiguation algorithm for reads aligned to human and mouse genomes using Tophat or BWA mem

dotfiles

null

exomeCov

utils functions for exome coverage plots as quality controls

flotilla

Reproducible machine learning analysis of gene expression and alternative splicing data

flycheck

Modern on the fly syntax checking for GNU Emacs

fusion-gene-blacklist

blacklist of fusion genes

geneimpacts

prioritize effects of variant annotations from VEP, SnpEff, et al.

gffcompare

classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF

gffutils

GFF and GTF file manipulation and interconversion

gffutils-utils

Collection of one off type scripts using a gffutils database

g-quad

Calculates the G-quadraplex score for a FASTA file of sequences

hera

null

hisat2

Graph-based alignment (Hierarchical Graph FM index)

homebrew

:beer: The missing package manager for OS X.

homebrew-cbl

Homebrew repository for CloudBioLinux: incubator for formulas to end up in homebrew-science

homebrew-science

:microscope: Scientific formulae for the Homebrew package manager

incanter

Clojure-based, R-like statistical computing and graphics environment for the JVM

indrops

Pipeline for processing inDrops sequencing data

ipyparallel

Interactive Parallel Computing in Python

ipython

Official repository for IPython itself. Other repos in the IPython organization contain things like the website, documentation builds, etc.

ipython-cluster-helper

Tool to easily start up an IPython cluster on different schedulers.

ISDB

A toolkit for creating databases of viral integration sites in host genomes

junkdrawer

collection of small scripts or how-tos that don't fall under a separate project

kallisto

Near-optimal RNA-Seq quantification

linuxbrew

A fork of Homebrew for Linux

miRge

miRge - microRNA alignment software for small RNA-seq data, now at v2.0

MISO

MISO: Mixture of Isoforms model for RNA-Seq isoform quantitation

miso-hg38-events

hg38 event level annotations for use with MISO, translated from hg19 from Crossmap.

mjw-toolbox

a phial of holy water, one stained priest's collar, and a single sandalwood-handled six shooter.

monocle-release

null

MultiQC

Aggregate results from bioinformatics analyses across many samples into a single report.

MultiQC_bcbio

MultiQC plugin for bcbio_nextgen pipeline

MultiQC_TestData

Test data for MultiQC. See https://github.com/ewels/MultiQC

mypubs

creation of methods with the purpose of tools comparison

NMF

NMF: A Flexible R package for Nonnegative Matrix Factorization

normpy

Normalization methods for RNA-Seq expression data in Python.

os-x-otp-token-paster

Paste the current one-time password (OTP) into the current iTerm window

peddy

genotype :: ped correspondence check, ancestry check, sex check. directly, quickly on VCF

PitchWeather

Links Weather Underground weather data to a PitchFx database

pizzly

Fast fusion detection using kallisto

polyester

Bioconductor package "polyester", devel version. RNA-seq read simulator.

prelude

Prelude is an enhanced Emacs 24 configuration that should make your experience with Emacs both more pleasant and more powerful.

python-gcon

Python API for interacting with several genomics storage solutions.

python-humbug

API bindings for Humbug

quantum-diceware

Diceware random password generation using the ANU quantum random number server as the randomness source

Quarkeon-Express

HParty 2011 hackathon project

radwa-bedtools-hiv

null

RapMap

Rapid sensitive and accurate read mapping via quasi-mapping

r-assertive.datetimes-feedstock

A conda-smithy repository for r-assertive.datetimes.

r-assertive-feedstock

A conda-smithy repository for r-assertive.

r-clisymbols-feedstock

A conda-smithy repository for r-clisymbols.

rlsim

A package for simulating RNA-seq library preparation with parameter estimation

rna-editing-classifier

Classify A->I RNA editing events from RNA-seq variants

RNASeqReadSimulator

RNASeqReadSimulator is a simple tool to generate simulated single-end or paired-end RNA-Seq reads.

roryk.github.io

null

r-rcurl-feedstock

A conda-smithy repository for r-rcurl.

r-rdrop2-feedstock

A conda-smithy repository for r-rdrop2.

r-sessioninfo-feedstock

A conda-smithy repository for r-sessioninfo.

rubin-cell-fate-conversion

Analysis scripts for the Rubin lab's cell fate conversion experiment

r-viridis-feedstock

A conda-smithy repository for r-viridis.

r-viridislite-feedstock

A conda-smithy repository for r-viridislite.

salmon

Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using lightweight alignments

salmon-cwl

Example CWL workflow for running Salmon

sambamba

Tools for working with SAM/BAM data

scde

R package for analyzing single-cell RNA-seq data

schema_salad

Semantic Annotations for Linked Avro Data

seurat

R toolkit for single cell genomics

sickle

Windowed Adaptive Trimming for fastq files using quality

simple-rnaseq-sim

null

singlecell

single-cell data analysis incubator

singlecell-barcodes

whitelisted singlecell barcodes and information regarding where molecular/sample/cellular barcodes are in each read, for various singlecell protocols

sleuth

Inspect kallisto RNA-Seq output

spacemacs

Emacs advanced Kit focused on Evil: The best editor is neither Emacs nor Vim, it's Emacs *and* Vim!

spacemacs-private

private layers for spacemacs

spliced-blog

data for the -spliced- blog

spp-idr

Wrappers around NGS peak callers to both call peaks and run IDR

staged-recipes

A place to submit conda recipes before they become fully fledged conda-forge feedstocks

tcrbiter

tcrbiter

themeTest

SinglePaged - Simple Jekyll template

tiny-test-data

Super small biological datasets for unit testing

toolz

A functional standard library for Python.

tophat-recondition

Post-processor for TopHat unmapped.bam files making them useable by downstream software.

Training-modules

Materials for short, half-day workshops

transrate

Understand your transcriptome assembly

umis

null

UPKUtils

Set of utilities to work with UPK files

vagrant_boxes

development boxes

varistran

R package providing Variance Stabilizing Transformations appropriate for RNA-Seq data

varistran-review

null

vcf2db

create a gemini-compatible database from a VCF

vcfanno

annotate a VCF with other VCFs/BEDs/tabixed files

venter_response

null

xcom_nicknames

Utility to generate nicknames for X-Com Enemy Unknown

Commits To