15 Repositories
Python 3d-genome Libraries
A spatial genome aligner for analyzing multiplexed DNA-FISH imaging data.
jie jie is a spatial genome aligner. This package parses true chromatin imaging signal from noise by aligning signals to a reference DNA polymer model
9 Sep 29, 2022
A sage package for working with circular genomes represented by signed or unsigned permutations
Circular genome tools (cgt) A sage package for working with circular genomes represented by signed or unsigned permutations. It includes tools for con
1 Mar 10, 2022
Gapmm2: gapped alignment using minimap2 (align transcripts to genome)
gapmm2: gapped alignment using minimap2 This tool is a wrapper for minimap2 to r
2 Jan 27, 2022
Pipeline code for Sequential-GAM(Genome Architecture Mapping).
Sequential-GAM Pipeline code for Sequential-GAM(Genome Architecture Mapping). mapping whole_preprocess.sh include the whole processing of mapping. usa
3 Nov 3, 2022
Train Scene Graph Generation for Visual Genome and GQA in PyTorch = 1.2 with improved zero and few-shot generalization.
Scene Graph Generation Object Detections Ground truth Scene Graph Generated Scene Graph In this visualization, woman sitting on rock is a zero-shot tr
93 Dec 28, 2022
Bottom-up attention model for image captioning and VQA, based on Faster R-CNN and Visual Genome
bottom-up-attention This code implements a bottom-up attention model, based on multi-gpu training of Faster R-CNN with ResNet-101, using object and at
1.3k Jan 9, 2023
Retrieve annotated intron sequences and classify them as minor (U12-type) or major (U2-type)
(intron I nterrogator and C lassifier) intronIC is a program that can be used to classify intron sequences as minor (U12-type) or major (U2-type), usi
4 Jul 26, 2022
These are the scripts used for the project of ‘Assembly of a pan-genome for global cattle reveals missing sequence and novel structural variation, providing new insights into their diversity and evolution history’
script-SV-genotyping These are the scripts used for the project of ‘Assembly of a pan-genome for global cattle reveals missing sequence and novel stru
2 Aug 26, 2022
Replace sequence_IDs in gff3 based on given genome.fasta
gff-rename Replace the sequence IDs in a gff3 file with a set of provided sequence IDs from a genom.fasta. This is useful when a gff3 file is retrieve
1 Nov 12, 2021
cLoops2: full stack analysis tool for chromatin interactions
cLoops2: full stack analysis tool for chromatin interactions Introduction cLoops2 is an extension of our previous work, cLoops. From loop-calling base
25 Dec 14, 2022
CBMPy Metadraft: a flexible and extensible genome-scale model reconstruction tool
CBMPy Metadraft: a flexible and extensible, GUI-based genome-scale model reconstruction tool that supports multiple Systems Biology standards.
1 Mar 14, 2022
Identify and annotate mutations from genome editing assays.
CRISPR-detector Here we propose our CRISPR-detector to facilitate the CRISPR-edited amplicon and whole genome sequencing data analysis, with functions
2 Feb 20, 2022
Code for "Learning Canonical Representations for Scene Graph to Image Generation", Herzig & Bar et al., ECCV2020
Learning Canonical Representations for Scene Graph to Image Generation (ECCV 2020) Roei Herzig*, Amir Bar*, Huijuan Xu, Gal Chechik, Trevor Darrell, A
24 Jul 7, 2022
minimizer-space de Bruijn graphs (mdBG) for whole genome assembly
rust-mdbg: Minimizer-space de Bruijn graphs (mdBG) for whole-genome assembly rust-mdbg is an ultra-fast minimizer-space de Bruijn graph (mdBG) impleme
148 Dec 1, 2022
To be a next-generation DL-based phenotype prediction from genome mutations.
Sequence -----------+-- 3D_structure -- 3D_module --+ +-- ? | |
18 Jan 11, 2022