Pinned Repositories
ampcorrect
Software for correcting and collapsing long read sequenced amplicons
EEL
Enhancer Element Locator
finfamily
A general purpose genealogy software
gcf52ref
GpC methylation from fast5:s to reference anchored calls
huddinge_tsne_browser
Tool to browse sequence kmers laid out in 2D with TSNE approximating Huddinge distance
pyhuddinge
Computing Huddinge distance with python call.
SLRP
Systematic Long Range Phasing
VirusIntegrationFinder
Finding virus integration sites from whole genome nanopore sequence
kpalin's Repositories
kpalin/gcf52ref
GpC methylation from fast5:s to reference anchored calls
kpalin/huddinge_tsne_browser
Tool to browse sequence kmers laid out in 2D with TSNE approximating Huddinge distance
kpalin/VirusIntegrationFinder
Finding virus integration sites from whole genome nanopore sequence
kpalin/bam_to_mods
kpalin/bioconda-recipes
Conda recipes for the bioconda channel.
kpalin/biopython
Official git repository for Biopython (originally converted from CVS)
kpalin/bioservices
kpalin/cookiecutter-data-science
A logical, reasonably standardized, but flexible project structure for doing and sharing data science work.
kpalin/cuddlySV
Long read based human genomic structural variation detection with cuteSV
kpalin/igv.js
Embeddable genomic visualization component based on the Integrative Genomics Viewer
kpalin/LDI-PCR-call
Software for calling insertions from long read sequenced LDI-PCR reads
kpalin/learn_rust
kpalin/longshot
diploid SNV caller for error-prone reads
kpalin/MultiQC
Aggregate results from bioinformatics analyses across many samples into a single report.
kpalin/MultiQC_TestData
Test data for MultiQC. See https://github.com/ewels/MultiQC
kpalin/nanoget
Functions to extract information from Oxford Nanopore sequencing data and alignments
kpalin/ont2cram
Oxford Nanopore HDF/Fast5 to CRAM conversion tool
kpalin/ONT_hg_somatic
Somatic variant calling for ONT WGS cancer data
kpalin/pyrexact2x2
kpalin/pysam
Pysam is a Python module for reading and manipulating SAM/BAM/VCF/BCF files. It's a lightweight wrapper of the htslib C-API, the same one that powers samtools, bcftools, and tabix.
kpalin/r-base-feedstock
A conda-smithy repository for r-base.
kpalin/rsfibreseq
kpalin/seaborn
Statistical data visualization using matplotlib
kpalin/seqtk
Toolkit for processing sequences in FASTA/Q formats
kpalin/somalier
fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs
kpalin/staged-recipes
A place to submit conda recipes before they become fully fledged conda-forge feedstocks
kpalin/vbz_compression
VBZ compression plugin for nanopore signal data
kpalin/vcfctx
VCF mutation context analysis scripts
kpalin/wf-somatic-variation
kpalin/xpore
Identification of differential RNA modifications from nanopore direct RNA sequencing