Flatiron Institute

Repositories

• q2-matchmaker

  A qiime2 plugin for case-control differential abundance analysis
  Python BSD-3-Clause 1 2 11 1 Updated Jul 31, 2021

• spack

  Forked from spack/spack

  A flexible package manager that supports multiple versions, configurations, platforms, and compilers.
  Python 1,379 0 0 0 Updated Jul 31, 2021

• solid_dmft

  solid_dmft is a versatile python wrapper to perform DFT+DMFT calculations utilizing the TRIQS software library.

  solid-state-physics dmft correlated-electrons
  Python 0 0 0 0 Updated Jul 31, 2021

• triqs_spectrometer

  triqs spectral function analyzer
  Python GPL-3.0 0 0 0 0 Updated Jul 30, 2021

• SkellySim
  Python Apache-2.0 1 1 0 0 Updated Jul 30, 2021

• inferelator

  Task-based gene regulatory network inference using single-cell or bulk gene expression data conditioned on a prior network.

  network inference
  Python BSD-2-Clause 8 17 4 0 Updated Jul 30, 2021

• spikeforest

  Spike sorting benchmarking system
  Python Apache-2.0 1 1 3 0 Updated Jul 30, 2021

• fmm2d

  This codebase is a set of libraries to compute N-body interactions governed by the Laplace and Helmholtz equations, to a specified precision, in two dimensions, on a multi-core shared-memory machine.
  Fortran Apache-2.0 1 10 0 0 Updated Jul 30, 2021

• FMM3D

  Flatiron Institute Fast Multipole Libraries --- This codebase is a set of libraries to compute N-body interactions governed by the Laplace and Helmholtz equations, to a specified precision, in three dimensions, on a multi-core shared-memory machine.
  Fortran 14 50 4 1 Updated Jul 30, 2021

• q2-batch

  Quick and dirty batch effect estimation in qiime2
  Python BSD-3-Clause 1 0 1 1 Updated Jul 29, 2021

• cpp2doc_webdemo

  Documentation site for TRIQS.
  SCSS 0 0 0 1 Updated Jul 29, 2021

• hither

  Run batches of Python functions in containers and on remote servers
  Python Apache-2.0 1 3 28 1 Updated Jul 26, 2021

• labbox-ephys
  TypeScript 5 3 14 6 Updated Jul 26, 2021

• DeepFRI

  Deep functional residue identification

  machine-learning deep-learning tensorflow protein-data-bank gene-ontology graph-convolutional-networks class-activation-maps
  Python BSD-3-Clause 11 48 2 0 Updated Jul 25, 2021

• SlurmUtil

  slurm monitoring tools and interface
  Python 0 4 10 0 Updated Jul 23, 2021

• CaImAn

  Computational toolbox for large scale Calcium Imaging Analysis, including movie handling, motion correction, source extraction, spike deconvolution and result visualization.

  calcium-imaging motion-correction source-extraction deconvolution 2-photon cnmf
  Jupyter Notebook GPL-2.0 273 399 35 1 Updated Jul 23, 2021

• catvae

  Categorical Variational Autoencoders
  Jupyter Notebook BSD-3-Clause 1 3 10 (1 issue needs help) 0 Updated Jul 23, 2021

• fastqToMat0

  Tools for extracting and mapping transcriptional barcodes from single-cell sequencing reads
  Python MIT 1 1 0 0 Updated Jul 21, 2021

• disBatch

  Driver script (python) to distribute a batch of tasks over a collection of compute nodes.
  Python Apache-2.0 4 15 8 0 Updated Jul 21, 2021

• flathub

  A simple elasticsearch frontend for serving astrophysical simulation catalog data
  Jupyter Notebook Apache-2.0 2 6 20 0 Updated Jul 21, 2021

• mouse_embryo_labeller

  A tool for tracking mouse embryo cell nuclei over time using data derived from 4d microscopy
  Python Apache-2.0 0 0 0 0 Updated Jul 21, 2021

• finufft

  Non-uniform fast Fourier transform library of types 1,2,3 in dimensions 1,2,3
  C++ 40 106 14 (2 issues need help) 2 Updated Jul 21, 2021

• learn-sciware-dev

  Learning materials for scientific software development
  HTML 18 26 1 0 Updated Jul 20, 2021

• st_gridnet

  A Python implementation of the model described in our publication "A convolutional neural network for common-coordinate registration of high-resolution histology images" developed principally for applications to registration of spatial transcriptomics image data.

  neural-networks image-registration spatial-transcriptomics tissue-registration visium-st
  Python 1 9 0 0 Updated Jul 20, 2021

• ccq-software-build

  CCQ software build scripts
  Shell 1 3 0 0 Updated Jul 19, 2021

• feedWebGL2

  Tools for implementing WebGL2 feedback processing stages for graphics preprocessing or other purposes
  JavaScript BSD-2-Clause 1 0 1 7 Updated Jul 19, 2021

• cufinufft

  Nonuniform fast Fourier transforms of types 1 and 2, in 2D and 3D, on the GPU
  Cuda 7 45 12 (1 issue needs help) 1 Updated Jul 12, 2021

• sparse_dot

  Python wrapper for Intel Math Kernel Library (MKL) matrix multiplication

  python numpy matrix-multiplication sparse scipy sparse-matrix mkl
  Python MIT 5 28 3 0 Updated Jul 6, 2021

• boxcodes3d

  This repository contains box codes for evaluating volume potentials for Laplace, Helmholtz, Maxwell, and Stokes
  Fortran 0 4 0 0 Updated Jul 4, 2021

• isosplit5

  ISO-SPLIT clustering (stand-alone version)
  C++ 3 6 2 0 Updated Jun 18, 2021