alimanfoo

Malaria Vector Surveillance Lead at the Wellcome Sanger Institute, Genomic Surveillance Unit.

Wellcome Sanger InstituteBerkshire, UK

Pinned Repositories

csvvalidator
A small CSV validator library for Python.
Language:Python81 7 1248
numpydoc_decorator
Build numpy-style docstrings programmatically and apply them using a decorator.
Language:Python16 3 101
pysamstats
A fast Python and command-line utility for extracting simple statistics against genome positions based on sequence alignments from a SAM or BAM file.
Language:Python192 12 10043
vcfnp
Load numpy arrays and HDF5 files from VCF (variant call format)
Language:Python31 7 528
zarrita
Language:Python17 8 189
scikit-allel
A Python package for exploring and analysing genetic variation data
Language:Jupyter Notebook289 25 26351
malariagen-data-python
Analyse MalariaGEN data from Python
Language:Jupyter Notebook14 8 34624
thereisnocourse
Language:Python0 1 10
zarr-python
An implementation of chunked, compressed, N-dimensional arrays for Python.
Language:Python1.6k 45 934290

alimanfoo's Repositories

alimanfoo/vcfnp
Load numpy arrays and HDF5 files from VCF (variant call format)
Language:Python31 7 528
alimanfoo/octopus
Bayesian haplotype-based mutation calling
Language:C++1
alimanfoo/agam-kilifi-report-2017
Language:Jupyter Notebook
alimanfoo/agam-report-base
Language:Python
alimanfoo/allel-model-algos
Data model algorithms for genome variation data.
alimanfoo/bcolz
A columnar data container that can be compressed.
Language:C
alimanfoo/bcolz-feedstock
A conda-smithy repository for bcolz.
Language:Shell
alimanfoo/bioconda-recipes
Conda recipes for the bioconda channel.
Language:Shell
alimanfoo/dask
Parallel computing with task scheduling
Language:Python
alimanfoo/dask-feedstock
A conda-smithy repository for dask.
Language:Shell
alimanfoo/dask-kubernetes
Native Kubernetes integration for dask
Language:Python
alimanfoo/datalab-image
Defines the default user image and environment for MalariaGEN DataLab.
Language:Dockerfile2 0
alimanfoo/fasteners-feedstock
A conda-smithy repository for fasteners.
Language:Shell
alimanfoo/genomics-benchmarks
Benchmarking of systems for storage and compute over large-scale genomic data
Language:Jupyter Notebook
alimanfoo/monotonic-feedstock
A conda-smithy repository for monotonic.
Language:Shell
alimanfoo/numcodecs
A Python package providing buffer compression and transformation codecs for use in data storage and communication applications.
Language:Python1
alimanfoo/numcodecs-feedstock
A conda-smithy repository for numcodecs.
Language:Shell
alimanfoo/panoptes
Eyes on your (genomic) data
Language:JavaScript
alimanfoo/petl-feedstock
A conda-smithy repository for petl.
Language:Python
alimanfoo/pytables-feedstock
A conda-smithy repository for pytables.
Language:Shell
alimanfoo/repo2docker
Turn git repositories into Jupyter enabled Docker Images
Language:Python
alimanfoo/scikit-allel-feedstock
A conda-smithy repository for scikit-allel.
Language:Shell
alimanfoo/skallel
Meta-package providing access to all scikit-allel functions via a single namespace.
Language:Python
alimanfoo/slides
A template for slides using markdown
Language:Makefile
alimanfoo/staged-recipes
A place to submit conda recipes before they become fully fledged conda-forge feedstocks
Language:Python
alimanfoo/tskit-workshop
JupyterHub infrastructure for tskit workshops
Language:Jupyter Notebook
alimanfoo/user_guide
The CWL v1.0 user guide
Language:HTML3 0
alimanfoo/vcflib
a simple C++ library for parsing and manipulating VCF files
Language:C++
alimanfoo/zarr-developers.github.io
Zarr blog
Language:JavaScript2 0
alimanfoo/zarr-feedstock
A conda-smithy repository for zarr.
Language:Shell