Pinned Repositories
sarge
Heuristic, parsimony-based ancestral recombination graph inference
ad-libs
local ancestry inference tool for low-coverage resequencing data
cellbouncer
Tools for pooled single cell sequencing experiments: demultiplex cells, infer doublet rate, assign treatments/sgRNAs, infer ambient RNA from allele matching
litterbox
Clean up CAT (Comparative Annotation Toolkit) annotations
bio_misc
Miscellaneous bioinformatics-related stuff
dropbox-sdk-python
Python SDK for Dropbox API v2.
htswrapper
Collection of handy things for code dealing with high throughput sequencing data
mixtureDist
A fast and flexible C++ library for Expectation-Maximization fitting of mixture models
numty-dumpty
Prepare genome for use in scATAC analysis by finding and masking possible NUMTs, throwing away small scaffolds, and creating a BED file of unmappable regions
optimML
A fast and flexible C++ library for numeric optimization of complex log likelihood functions, including mixture components that must sum to 1
nkschaefer's Repositories
nkschaefer/cellbouncer
Tools for pooled single cell sequencing experiments: demultiplex cells, infer doublet rate, assign treatments/sgRNAs, infer ambient RNA from allele matching
nkschaefer/mixtureDist
A fast and flexible C++ library for Expectation-Maximization fitting of mixture models
nkschaefer/optimML
A fast and flexible C++ library for numeric optimization of complex log likelihood functions, including mixture components that must sum to 1
nkschaefer/htswrapper
Collection of handy things for code dealing with high throughput sequencing data
nkschaefer/stlbfgs
C++ L-BFGS implementation using plain STL
nkschaefer/litterbox
Clean up CAT (Comparative Annotation Toolkit) annotations
nkschaefer/numty-dumpty
Prepare genome for use in scATAC analysis by finding and masking possible NUMTs, throwing away small scaffolds, and creating a BED file of unmappable regions
nkschaefer/bio_misc
Miscellaneous bioinformatics-related stuff
nkschaefer/py-multi-seq
Python implementation of MULTIseq barcode alignment using fuzzy string matching and GMM barcode assignment.
nkschaefer/ad-libs
local ancestry inference tool for low-coverage resequencing data
nkschaefer/scrna-parameter-estimation
Direct estimation of mean and covariance from single cell RNA seq experiments
nkschaefer/sarge
Heuristic, parsimony-based ancestral recombination graph inference
nkschaefer/SparK
Publication quality NGS track plotting
nkschaefer/dropbox-sdk-python
Python SDK for Dropbox API v2.
nkschaefer/ucscthesis
LaTeX templates for UCSC thesis and/or advancement (thesis proposal)
nkschaefer/preseq
Software for predicting library complexity and genome coverage in high-throughput sequencing.