Kamil Slowikowski

ggrepel. :round_pushpin: Repel overlapping text labels away from each other in your ggplot2 figures.

harmonypy. 🎼 Integrate multiple high-dimensional datasets with fuzzy k-means and locally linear adjustments.

awesome-vdj. 📚 Tools and databases for analyzing HLA and VDJ genes.

snakefiles. :snake: Snakefiles for common RNA-seq data analysis workflows (STAR and Kallisto).

tftargets. :dart: Human transcription factor target genes from 6 databases in convenient R format.

pytabix. :card_index: Retrieve data in genomic intervals with a Python interface for tabix.

picardmetrics. :vertical_traffic_light: Run Picard on BAM files and collate 90 metrics into one file.

snpsea. :bar_chart: Identify cell types and pathways affected by genetic risk loci.

cellguide. 🧭 Navigate single-cell RNA-seq datasets in your web browser.

proxysnps. :bookmark: Get SNP proxies from the 1000 Genomes Project.

CENTIPEDE.tutorial. :bug: How to use CENTIPEDE to determine if a transcription factor is bound.

allelefrequencies. 📂 HLA allele frequencies in tab-delimited format, downloaded from AFND.

hlabud. 🐶 hlabud: HLA genotype analysis in R

homerkit. Read HOMER motif analysis output in R.

snpbook. :orange_book: Explore 1000 Genomes variant data with JavaScript.

fibrotime. :tangerine: View the gene expression response to TNF and IL-17A with vanilla Javascript and HTML.

saturation. :sponge: Estimate sequencing saturation for GEX, VDJ, and ADT data from the 10x Genomics platform.

circles. :rainbow:

xlmhg. :chart_with_downwards_trend: Non-parametric rank enrichment test for binary data.

pubmed-pairs. ✌️ Search PubMed for each pair of terms from two lists.

dotfiles. Kamil's dotfiles

slowkow.com. Personal website.

fern. :herb: Barnsley fern

covid-stats. New daily Covid cases and deaths in USA. Data from usafacts.org

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

awesome-expression-browser. 😎 A curated list of software and resources for exploring and visualizing (browsing) expression data 😎

highcharter. R wrapper for highcharts based on htmlwidgets

wiggleplotr. A small R package to make sequencing read coverage plots in R.

seurat. R toolkit for single cell genomics

MERmaid. WebGL-based viewer for MERFISH data

authorbud. 🐶 Make an author page by dragging and dropping a table.

arrayqc. Quality control metrics for microarray data.