Pinned Repositories
zstd
Zstandard - Fast real-time compression algorithm
bam-lorenz-coverage
Generate Lorenz plots and Coverage plots directly from BAM files
dr-disco
:mask::loudspeaker: Dr. Disco: detecting genomic breakpoints of fusion transcripts in random hexamer RNA-seq data
egfr-v3-determiner
Free open-source tool to extract counts of spliced EGFR vIII / EGFR non-vIII (wt) reads
fastafs
toolkit for file system virtualisation of random access compressed FASTA, FAI, DICT & TWOBIT files
flaimapper
:honeybee: Fragment Location Annotation Identification Mapper: computational annotation of small ncRNA-derived fragments using RNA-seq high-throughput data
fuma
:dash::leopard: FuMa: reporting overlap in RNA-seq detected fusion genes
gsam
gsam
pymnp
Python 3 API and batch downloader/re-runner for the MolecularNeuropathology brain classifier
recursiveCorPlot
Recursive correlation based natural clustering (using ggplot, labels and historgrams)
yhoogstrate's Repositories
yhoogstrate/fastafs
toolkit for file system virtualisation of random access compressed FASTA, FAI, DICT & TWOBIT files
yhoogstrate/bam-lorenz-coverage
Generate Lorenz plots and Coverage plots directly from BAM files
yhoogstrate/flaimapper
:honeybee: Fragment Location Annotation Identification Mapper: computational annotation of small ncRNA-derived fragments using RNA-seq high-throughput data
yhoogstrate/fuma
:dash::leopard: FuMa: reporting overlap in RNA-seq detected fusion genes
yhoogstrate/gsam
gsam
yhoogstrate/recursiveCorPlot
Recursive correlation based natural clustering (using ggplot, labels and historgrams)
yhoogstrate/dr-disco
:mask::loudspeaker: Dr. Disco: detecting genomic breakpoints of fusion transcripts in random hexamer RNA-seq data
yhoogstrate/egfr-v3-determiner
Free open-source tool to extract counts of spliced EGFR vIII / EGFR non-vIII (wt) reads
yhoogstrate/pymnp
Python 3 API and batch downloader/re-runner for the MolecularNeuropathology brain classifier
yhoogstrate/scRNA-glioma-project
single-cell and single-nucleus RNA-seq analysis of public data
yhoogstrate/scRNA-glioma-workflows
Workflows for the processing of public and in-house spatial and/or single cell/nucleus RNA-seq glioma datasets
yhoogstrate/bioconda-recipes
Conda recipes for the bioconda channel.
yhoogstrate/segmentation-fold
:triangular_ruler: segmentation-fold: RNA folding including K-turns
yhoogstrate/bio-kernel
Official landing place of the bio-kernel project
yhoogstrate/cmatrix
Terminal based "The Matrix" like implementation
yhoogstrate/disc-art
Disc-Art - some kind of omics artifact analyser
yhoogstrate/ega-upload
README how to upload seq data into EGA
yhoogstrate/fibronectin-splice-variant-detector
fibronectin-splice-variant-detector
yhoogstrate/geomnet
Examples and data for geom_net
yhoogstrate/glass-nl
GLASS-NL RNA-seq
yhoogstrate/glass-od
glass-od
yhoogstrate/idat-tools
Application to mix idat files (e.g. tumor with normal)
yhoogstrate/naf
Nucleotide Archival Format - Compressed file format for DNA/RNA/protein sequences
yhoogstrate/pymetharray
Modified fork of "Python-based preprocessing software for Illumina methylation arrays"
yhoogstrate/sc_seurat
Scripts for single-cell 'omics analysis
yhoogstrate/snoekdobber3d
3D printer modellen voor snoekdobbers
yhoogstrate/SoupX
R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data
yhoogstrate/staged-recipes
A place to submit conda recipes before they become fully fledged conda-forge feedstocks
yhoogstrate/tacc3-fgfr3-bam-quick-scanner
Quick scan for reads mapped to both TACC3 and FGFR3 in order to find fusions
yhoogstrate/vg
tools for working with variation graphs