bradhamlab Goto Github PK
Type: Organization
Bio: Developmental biology lab at Boston University headed by Cynthia A. Bradham
Location: Boston, MA
bradhamlab's Projects
az-paper-analysis-code
Code for the DE and enricment analysis for the paper entitled Alizarin Red perturbs skeletal patterning and biomineralization via Catalase inhibition.
blender
Contains scripts for converting CSV files to Blender code
csv2blender
Convert a .csv file of embryo coordinates to a blender model.
dbd_comparison
repository for comparing DNA Binding Sites for motif selection
ethanol_2022
Pipeline to analyze RNAseq data from Rodriguez-Sastre 2022
hcr_quantify
Quantify signal in HCR FISH images
icat
Identifying Cell-states Across Treatments
icat_manuscript
All analysis performed during the generation of the manuscript "ICAT: A Novel Algorithm to Robustly Identify Cell States Following Perturbations in Single Cell Transcriptomes"
image_scripts
Script for easy image processing
indrops
Pipeline for processing inDrops sequencing data
indrops-star
Pipeline to analyze Indrops V3 data using STARsolo
lv_anno_extend
Extend Lvar 3.0 genome annotations to include ribosomal + mitochondrial genes
lvar3_extract
Extract desired sequences from the Lvar3.0 genome
lverage
Motif Finder pipeline - searching for motifs through orthologous species.
ncfs
Modified NCFS algorithm for neighbor-based feature selection
oif
Extract images and metadata from .oif files.
pmc_detection
Workflow for detecting PMCs in confocal images
point_anno
Annotate 3-dimensional points in embryos using napari.
scpipe
Pipeline for scRNAseq read alignment
sslouvain
Forked from https://github.com/vtraag/louvain-igraph
transpipe
Pipeline for denova assembly of a transcriptome.
utr-extend
Extend 3' UTR annotations in a given genome using 3' sequencing reads
vnet.pytorch
A PyTorch implementation for V-Net: Fully Convolutional Neural Networks for Volumetric Medical Image Segmentation
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