Pinned Repositories
10x-scATAC-2019
Publication Page for Satpathy*, Granja* et al 2019
affymetrix-power-tools
AfterQC
Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
alfred
BAM Statistics, Feature Counting and Annotation
alpine
Modeling and correcting fragment sequence bias for RNA-seq
combat.py
python / numpy / pandas / patsy version of ComBat for removing batch effects.
hrk2109's Repositories
hrk2109/alfred
BAM Statistics, Feature Counting and Annotation
hrk2109/ascat
ASCAT copy number R package
hrk2109/awesome-single-cell
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
hrk2109/bestNormalize
Estimate a suite of normalizing transformations, including a new adaptation of a technique based on ranks which can guarantee normally distributed transformed data if there are no ties: ordered quantile normalization (ORQ).
hrk2109/biomartr
Genomic Data Retrieval with R
hrk2109/Blast2Bam
hrk2109/chimaera-1
Implementation of the Chimaera algorithm
hrk2109/cluster_diffex2018
scRNA-seq clustering, visualization, and differential expression pipeline from Sims Lab papers
hrk2109/COVID-19
Novel Coronavirus (COVID-19) Cases, provided by JHU CSSE
hrk2109/cTPnet
cTPnet Package
hrk2109/cytokit
Microscopy Image Cytometry Toolkit
hrk2109/DeepLearningCyTOF
hrk2109/demeter2
Inference of gene dependency from RNAi screening datasets.
hrk2109/EaCoN
Easy Copy Number !
hrk2109/fgsea
Fast Gene Set Enrichment Analysis
hrk2109/GenVisR
Genome data visualizations
hrk2109/HPAanalyze
A Bioconductor package to retrieve and analyze data from the Human Protein Atlas
hrk2109/ImcSegmentationPipeline
A pixelclassification based multiplexed image segmentation pipeline
hrk2109/In-depth-NGS-Data-Analysis-Course
Materials for 12-day course on analyzing RNA-Seq, ChIP-Seq and variant calling data.
hrk2109/lumpy-sv
lumpy: a general probabilistic framework for structural variant discovery
hrk2109/macOSLucidaGrande
A small utility to set customize your Mac's system UI font without modifying system files.
hrk2109/Molecular-Data-Science
FOS course Molecular Data Science
hrk2109/scRNA-seq-pipelines
Compendium to "A Systematic Evaluation of Single Cell RNA-Seq Analysis Pipelines"
hrk2109/scRNA.seq.course
Analysis of single cell RNA-seq data course
hrk2109/smartseq2
A pipeline for processing single cell RNA-seq data generated with the SmartSeq2 protocol.
hrk2109/tracer
TraCeR - reconstruction of T cell receptor sequences from single-cell RNAseq data
hrk2109/tutorials
Tutorials covering various topics in genomic data analysis.
hrk2109/UpSetR
An R implementation of the UpSet set visualization technique published by Lex, Gehlenborg, et al..
hrk2109/vitae
R Markdown Résumés and CVs
hrk2109/xgboost
Scalable, Portable and Distributed Gradient Boosting (GBDT, GBRT or GBM) Library, for Python, R, Java, Scala, C++ and more. Runs on single machine, Hadoop, Spark, Flink and DataFlow