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Budhaditya Basu (bio-visualisation)

bio-visualisation

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Company:University of Iowa

Location:Iowa City, IA, US

Home Page:https://bio-visualisation.github.io/bio-quarto/

Twitter:@VizBio

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Budhaditya Basu's starred repositories

CnRAP

Analytical pipeline developed to anlayze Cut and Run data. Inspired by both Henikoff (SEACR) and Orkin (Cut&RunTools) lab pipelines.

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Wilson_Muto_NComm_2022

Containerized workflow for analysis of human diabetic kidney disease by snRNA-seq and snATAC-seq

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MAESTRO

Single-cell Transcriptome and Regulome Analysis Pipeline

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Sleep-deprivation-and-protein-translation-TRAP-seq

Code for upper quartile normalization and quadrant figures from the paper.

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Visium-SOR-mouse

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chatterjee2021_nr4a

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scriabin

Analysis of cell-cell communication at single-cell resolution

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paletter

build your palette from a picture √

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decoupleR

R package to infer biological activities from omics data using a collection of methods.

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TCGAbiolinks

TCGAbiolinks

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iSpatial

infer whole genome spatial transcriptome by integrating single cell RNAseq and spatial transcriptome

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circRNA-sponging

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parallel-fastq-dump

parallel fastq-dump wrapper

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Shell_Intro_for_Bioinformatics_STG

Intro to Shell for Bioinformatics - with STG examples

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UpSetR

An R implementation of the UpSet set visualization technique published by Lex, Gehlenborg, et al..

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ClusterFoldSimilarity

Calculate cluster similarity between clusters from different single cell datasets/batches/samples.

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ComplexHeatmap

Make Complex Heatmaps

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simplifyEnrichment

Simplify functional enrichment results

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Seurat.utils

Various utility functions for Seurat single-cell analysis

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SCP

An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.

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quarto-iconify

Use Iconify icons in HTML-based Quarto documents (over 200,000 open source vector icons)

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rstudio-server-conda

Run Rstudio Server in a conda environment

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rstudio-server-conda_share

rstudio on RCC

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rstudio-server

Singularity container for RStudio-Server.

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singularity-containers

Webinars&Tutorial on Containers on HPC and Cloud with Singularity

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Code_for_circSC

Analysis pipeline for our circSC manuscript

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hex-stickers

RStudio hex stickers

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GBMatlas

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SCENICprotocol

A scalable SCENIC workflow for single-cell gene regulatory network analysis

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knowledgebase

recipes that save time

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