Pinned Repositories
beanplot
Beanplots on the command-line via Python
boostnote-cli
A simple CLI for Boostnote notes.
distrobox-boxkit
A personalised distrobox image
elearningcollection
A collection of random and not so random online learning materials for biology, computation, and bioinformatics
genomics
Sphinx documentation source for a computational genomics tutorial.
genomics-tutorial
An introductory tutorial into genomics.
matplotlib_solarized
Simple python matplotlib colormaps based on the solarized color palette by Ethan Schoonover
metagenomics-scripts
refseq2kraken
Download refseq-genomic data and prepare it for Kraken
vcfcompile
Simple scripts to summarize variants.
sschmeier's Repositories
sschmeier/distrobox-boxkit
A personalised distrobox image
sschmeier/airrflow
B-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation framework
sschmeier/ANARCI
Antibody Numbering and Antigen Receptor ClassIfication
sschmeier/arcasHLA
Fast and accurate in silico inference of HLA genotypes from RNA-seq
sschmeier/boxkit
A blingier starting image for Toolbx and Distrobox.
sschmeier/calib
Calib clusters barcode tagged paired-end reads based on their barcode and sequence similarity.
sschmeier/CRISPRseek
Design of target-specific guide RNAs in CRISPR-Cas9, genome-editing systems
sschmeier/devbox
Instant, easy, and predictable development environments
sschmeier/DNAscent
Software for detecting regions of BrdU and EdU incorporation in Oxford Nanopore reads.
sschmeier/EpiNano
Detection of RNA modifications from Oxford Nanopore direct RNA sequencing reads (Liu*, Begik* et al., Nature Comm 2019)
sschmeier/eplot
sschmeier/exceRpt
Software for preprocessing, filtering, alignment, and reporting of smallRNA-seq datasets
sschmeier/how_are_we_stranded_here
Check strandedness of RNA-Seq fastq files
sschmeier/hyb
hyb: a bioinformatics pipeline for the analysis of CLASH (crosslinking, ligation and sequencing of hybrids) data
sschmeier/khmer
In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more
sschmeier/modbam2bed
sschmeier/nanocompore
RNA modifications detection from Nanopore dRNA-Seq data
sschmeier/nanocompore_pipeline
Nextflow pipeline for nanocompore analysis
sschmeier/paperless-ngx
A community-supported supercharged version of paperless: scan, index and archive all your physical documents
sschmeier/preseq
Software for predicting library complexity and genome coverage in high-throughput sequencing.
sschmeier/pz
Easily handle day to day CLI operation via Python instead of regular Bash programs. 🇺🇦 #supporting
sschmeier/shapemapper2
Public repository for ShapeMapper 2 releases
sschmeier/shirloc
pipeline to identify ribosomal shifts of transcripts from polysome profiling rna-seq data.
sschmeier/sicelore
Single Cell Long Read is a suite of tools dedicated to Cell barcode / UMI assignment and analysis of highly multiplexed single cell Nanopore long read sequencing data.
sschmeier/starcode
All pairs search and sequence clustering
sschmeier/thtools
A library for the analysis of toehold switch riboregulators created by the iGEM team City of London UK 2021.
sschmeier/toeholder
Team iGEM ULaval 2019 scripts for toehold design
sschmeier/vbz_compression
VBZ compression plugin for nanopore signal data
sschmeier/vzborg
Simple deduplicated encrypted backups for Proxmox
sschmeier/wf-isoforms