slowkow

Computational biologist. Using transcriptomics to learn about inflammation and cancer.

Mass General Brigham

Pinned Repositories

awesome-vdj
📚 Tools and databases for analyzing HLA and VDJ genes.
210 15 225
cellguide
🧭 Navigate single-cell RNA-seq datasets in your web browser.
Language:JavaScript27 4 14
ggrepel
:round_pushpin: Repel overlapping text labels away from each other in your ggplot2 figures.
Language:R1.2k 26 21296
harmonypy
🎼 Integrate multiple high-dimensional datasets with fuzzy k-means and locally linear adjustments.
Language:Python200 6 2623
hlabud
🐶 hlabud: HLA genotype analysis in R
Language:TeX16 3 30
pytabix
:card_index: Retrieve data in genomic intervals with a Python interface for tabix.
Language:C83 4 109
snakefiles
:snake: Snakefiles for common RNA-seq data analysis workflows (STAR and Kallisto).
Language:Python89 5 136
tftargets
:dart: Human transcription factor target genes from 6 databases in convenient R format.
Language:R86 10 419

slowkow's Repositories

slowkow/ggrepel
:round_pushpin: Repel overlapping text labels away from each other in your ggplot2 figures.
Language:R1.2k 26 21296
slowkow/awesome-vdj
📚 Tools and databases for analyzing HLA and VDJ genes.
210 15 225
slowkow/harmonypy
🎼 Integrate multiple high-dimensional datasets with fuzzy k-means and locally linear adjustments.
Language:Python200 6 2623
slowkow/snpsea
:bar_chart: Identify cell types and pathways affected by genetic risk loci.
Language:C++35 3 59
slowkow/cellguide
🧭 Navigate single-cell RNA-seq datasets in your web browser.
Language:JavaScript27 4 14
slowkow/allelefrequencies
📂 HLA allele frequencies in tab-delimited format, downloaded from AFND.
Language:Python19 4 32
slowkow/hlabud
🐶 hlabud: HLA genotype analysis in R
Language:TeX16 3 30
slowkow/saturation
:sponge: Estimate sequencing saturation for GEX, VDJ, and ADT data from the 10x Genomics platform.
Language:R5 2 01
slowkow/pubmed-pairs
✌️ Search PubMed for each pair of terms from two lists.
Language:JavaScript4 2 01
slowkow/slowkow.com
Personal website.
Language:HTML3 3 02
slowkow/covid-stats
New daily Covid cases and deaths in USA. Data from usafacts.org
Language:R1 2 0
slowkow/fern
:herb: Barnsley fern
Language:HTML1 3 0
slowkow/seurat
R toolkit for single cell genomics
Language:R1 2 01
slowkow/.github
1 0
slowkow/actions
GitHub Actions for the R community
Language:JavaScript1 0
slowkow/airway_allergic_asthma
Language:HTML1 0
slowkow/blog
Source code of my personal blog
Language:TypeScript2 0
slowkow/cumulus
Language:WDL2 0
slowkow/demuxEM
Demultiplexing cell/nucleus hashing data for single-cell genomics
Language:Python2 0
slowkow/harmony
Scalable integration of single cell RNAseq data for batch correction and meta analysis
Language:R2 01
slowkow/hist_thresh
Language:Jupyter Notebook2 0
slowkow/hpsc-ie
Data from the Health Protection Surveillance Center in Ireland
Language:R
slowkow/milwaukee-weather
Use Github Actions to automatically update a weather graph every day
Language:R2 0
slowkow/MWNN
Multi-modal Weighted Nearest Neighbors
Language:Python2 0
slowkow/pegasus
Language:Python2 0
slowkow/presto
Fast Wilcoxon and auROC
Language:R2 0
slowkow/rapids-single-cell-examples
Examples of single-cell genomic analysis accelerated with RAPIDS
Language:Jupyter Notebook2 01
slowkow/slowkow
3 0
slowkow/symphony
Efficient and precise single-cell reference atlas mapping with Symphony
Language:R2 0
slowkow/velocyto.R
RNA velocity estimation in R
Language:R2 01