slowkow/snakefiles

Stars
88
Rank 375,465 (Top 8 %)
Language
Python
License
MIT License
Created almost 9 years ago
Updated over 7 years ago

slowkow/snakefiles

slowkow

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🐍 Snakefiles for common RNA-seq data analysis workflows (STAR and Kallisto).

ggrepel

📍 Repel overlapping text labels away from each other in your ggplot2 figures.

awesome-vdj

📚 Tools and databases for analyzing HLA and VDJ genes.

harmonypy

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

tftargets

🎯 Human transcription factor target genes from 6 databases in convenient R format.

pytabix

📇 Retrieve data in genomic intervals with a Python interface for tabix.

picardmetrics

🚦 Run Picard on BAM files and collate 90 metrics into one file.

snpsea

📊 Identify cell types and pathways affected by genetic risk loci.

proxysnps

🔖 Get SNP proxies from the 1000 Genomes Project.

cellguide

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

CENTIPEDE.tutorial

🐛 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

📙 Explore 1000 Genomes variant data with JavaScript.

fibrotime

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

Jupyter Notebook

saturation

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

circles

xlmhg

📉 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.

arrayqc

Quality control metrics for microarray data.

covid-stats

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

fern

🌿 Barnsley fern