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    23 repositories

    • Lverage

      Public
      Motif Finder pipeline - searching for motifs through orthologous species.
      Python
      •
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated Oct 2, 2024Oct 2, 2024

    • AZ-paper-analysis-code

      Public
      Code for the DE and enricment analysis for the paper entitled Alizarin Red perturbs skeletal patterning and biomineralization via Catalase inhibition.
      R
      •0•0•0•0•Updated Jun 25, 2024Jun 25, 2024

    • sslouvain

      Public
      Forked from https://github.com/vtraag/louvain-igraph
      C++
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Jun 13, 2024Jun 13, 2024

    • ethanol_2022

      Public
      Pipeline to analyze RNAseq data from Rodriguez-Sastre 2022
      R
      •1•0•0•1•Updated Mar 11, 2024Mar 11, 2024

    • scPipe

      Public
      Pipeline for scRNAseq read alignment
      Python
      •
      Apache License 2.0
      •0•0•17•0•Updated Feb 7, 2024Feb 7, 2024

    • icat

      Public
      Identifying Cell-states Across Treatments
      machine-learningclusteringsemi-supervised-learningsingle-cellsingle-cell-rna-seqsingle-cell-analysisself-supervised-learning
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•4•1•0•Updated Oct 19, 2023Oct 19, 2023

    • dbd_comparison

      Public
      repository for comparing DNA Binding Sites for motif selection
      Python
      •0•0•0•0•Updated Jun 7, 2023Jun 7, 2023

    • indrops-star

      Public
      Pipeline to analyze Indrops V3 data using STARsolo
      alignmentstarsingle-cell-genomicssingle-cell-rna-seqindropssingle-cell-analysis
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•1•0•Updated Jun 6, 2023Jun 6, 2023

    • pmc_detection

      Public
      Workflow for detecting PMCs in confocal images
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•9•0•Updated May 31, 2023May 31, 2023

    • lvar3_extract

      Public
      Extract desired sequences from the Lvar3.0 genome
      Python
      •1•0•6•0•Updated Feb 10, 2023Feb 10, 2023

    • hcr_quantify

      Public
      Quantify signal in HCR FISH images
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Sep 28, 2022Sep 28, 2022

    • ncfs

      Public
      Modified NCFS algorithm for neighbor-based feature selection
      machine-learningfeature-selection
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•2•0•Updated Aug 16, 2022Aug 16, 2022

    • image_scripts

      Public
      Script for easy image processing
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Jun 3, 2022Jun 3, 2022

    • ICAT_manuscript

      Public
      All analysis performed during the generation of the manuscript "ICAT: A Novel Algorithm to Robustly Identify Cell States Following Perturbations in Single Cell Transcriptomes"
      single-cell-rna-seqsingle-cell-analysis
      Jupyter Notebook
      •0•0•1•0•Updated May 26, 2022May 26, 2022

    • lv_anno_extend

      Public
      Extend Lvar 3.0 genome annotations to include ribosomal + mitochondrial genes
      Python
      •0•0•0•0•Updated Feb 21, 2022Feb 21, 2022

    • point_anno

      Public
      Annotate 3-dimensional points in embryos using napari.
      Python
      •
      MIT License
      •0•0•0•0•Updated Sep 15, 2020Sep 15, 2020

    • utr-extend

      Public
      Extend 3' UTR annotations in a given genome using 3' sequencing reads
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Apr 24, 2020Apr 24, 2020

    • indrops

      Public
      Pipeline for processing inDrops sequencing data
      snakemakestarsingle-cellsingle-cell-rna-seqindropsurchin
      Python
      •42•0•2•0•Updated Feb 10, 2020Feb 10, 2020

    • transPipe

      Public
      Pipeline for denova assembly of a transcriptome.
      Python
      •
      Apache License 2.0
      •0•0•9•0•Updated Sep 12, 2018Sep 12, 2018

    • vnet.pytorch

      Public
      A PyTorch implementation for V-Net: Fully Convolutional Neural Networks for Volumetric Medical Image Segmentation
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •200•1•3•0•Updated Aug 9, 2018Aug 9, 2018

    • Blender

      Public
      Contains scripts for converting CSV files to Blender code
      Python
      •0•0•0•0•Updated Aug 8, 2018Aug 8, 2018

    • oif

      Public
      Extract images and metadata from .oif files.
      Python
      •0•0•0•0•Updated Jun 5, 2018Jun 5, 2018

    • csv2blender

      Public
      Convert a .csv file of embryo coordinates to a blender model.
      Python
      •0•0•0•0•Updated May 28, 2018May 28, 2018