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bankers2

A set of tools to create plotting files from subset counts in banker's sequenc order. I.e. helper scripts for the visualisation of count data across all possible subsets of a sample set.

bcftools

This is my own personal development repository for BCFtools. Check out the main repository at: https://github.com/samtools/bcftools

bioconda-recipes

Conda recipes for the bioconda channel.

bioconda-utils

Utilities for building and managing bioconda recipes

cargo

The Rust package manager

coin-or-cbc-feedstock

A conda-smithy repository for coin-or-cbc.

coin_cbc

Rust bindings to the CoinOR CBC MILP Solveur using the C API.

coincbc-feedstock

A conda-smithy repository for coincbc.

create-quant-seq-testing-dataset

A Snakemake workflow for (reproducibly) creating a QuantSeq 3' mRNA testing dataset that is both small enough to run in standard continuous integration testing environments, and large enough to produce (some reasonably) meaningful results.

create-sv-ci-testing-dataset

a mini snakemake workflow to produce structural variant testing dataset small enough for CI systems, but large enough to be meaningful

datavzrd

A tool to create visual HTML reports from collections of CSV/TSV tables

deeptools

Tools to process and analyze deep sequencing data.

demo-standardized-workflow

evaluate_varlociraptor_purity_estimation

A little snakemake workflow to evaluate the varlociraptor subcommand `estimate contamination`.

ggplot2_intro

A quick introduction into ggplot2, with ioslides produced from Rmarkdown

hopr

This is the development site for Hands-On Programming with R, a book that teaches how to program in R, with hands-on examples. Read the book at https://rstudio-education.github.io/hopr.

hts-specs

Specifications of SAM/BAM and related high-throughput sequencing file formats

htslib

C library for high-throughput sequencing data formats

jannovar

Annotation of VCF variants with functional impact and from databases (executable+library)

lsf

Snakemake profile for running jobs on an LSF cluster

media

Various media related scripts

microarrays-r

neofox

Annotation of mutated peptide sequences with published or novel potential neoantigen descriptors

prosic2

Version 2 of the PROSIC caller for somatic variants.

r-color-palettes

Comprehensive list of color palettes available in r

r4ds

R for data science: a book

rna-seq-conservative-fold-change-without-replicates

snakemake workflow to determine conservative fold changes between transcriptomic samples when no biological replicates are available

rna-seq-kallisto-sleuth

A workflow for RNA-seq differential expression analysis based on Kallisto and Sleuth.

rust-feedstock

A conda-smithy repository for rust.

rust-lp-modeler

Lp modeler written in Rust