geng-lee Goto Github PK

awesome-artificial-intelligence

A curated list of Artificial Intelligence (AI) courses, books, video lectures and papers.

awesome-shiny-apps-for-statistics

🌟 A curated list of Awesome Shiny Apps for Statistics (ASAS)🌟

bam-readcount

Count bases in BAM/CRAM files

bam-to-junction-bed

Uses SAMTools, Python 2.7 and PySam to extract either junctions or exon read counts for known and novel junctions and exons. Requires an indexed BAM file with genomic coordinates

base-editing-analysis

Short script for analyzing base-editing-outcomes in Dow Lab screen.

bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis

be-smart

A deep learning tool for CRISPR base editing efficiency prediction

be_predict_bystander

Deep conditional autoregressive models for genome editing sequence-to-sequence problems

be_predict_efficiency

beautiful-jekyll

✨ Build a beautiful and simple website in literally minutes. Demo at https://beautifuljekyll.com

belib_processing

Code for processing data from base editing screens performed with the libraries first described in Arbab, Shen, et al., Cell (2020). Contains code used for Neugebauer et al., Nat. Biotechnol. (2022)

benchmarking_variant_callers

In this study, we perform systematic comparative analysis of seven widely-used SNV-calling methods, including SAMtools, the GATK Best Practices pipeline, CTAT, FreeBayes, MuTect2, Strelka2 and VarScan2, on both simulated and real single-cell RNA-seq datasets. We evaluate the performances of these tools in different read depths, genomic contexts, functional regions and variant allele frequencies.

besensor

Files related to base editing sensor data and BE-SCAN Shiny app

biancur-cellmetabolism-2020

Corresponding code and figures for publication of Biancur DE, Kapner KS, Yamamoto K, Banh RS, Neggers JE, Sohn ASW, Wu W, Manguso R, Brown A, Root D, Aguirre AJ, Kimmelman AC. Functional Genomics Identifies Metabolic Vulnerabilities in Pancreatic Cancer. Cell Metabolism, 2020, In Press.

blog

seqyuan

breat-cancer-screening-classification-and-evaluation-using-confusion-matrix

This project was made for a client on PeoplePerHour. The data involves screening different columns and then plotting out confusion matrices using the Seaborn Library and HeatMaps. The True positives, False positives, True negatives, False negatives are calculated and then used to calculate specificity and sensitivity.

brspdata

Allen Institute BrainSpan Exon and Gene Expression Values

bsrpipline

Analysis Pipline Of Bulked Segregant RNA-Seq

bulk_rnaseq_course_base

capanno

cwl/wdl/sm/nf files, tool and workflow metadata, and input specifications.

cas-analyzer

Full JavaScript-based assessment tool for targeted sequencing data of genome-edited samples.

cell-state-atlas-2022

Code for a multimodal atlas of healthy and injured cell states and niches in the human kidney

cell_types_signatures

cerebro-paper

chip-seq-analysis

ChIP-seq analysis notes from Ming Tang

choices13k

circle_finder

Micro DNA identification

clam

Data Efficient & Weakly Supervised Computational Pathology on Whole Slide Images

cld

A software for the multispecies design of CRISPR/Cas9 libraries

clip