JD2112/10studAnalysis
R
⭐ 0
🍴 0
👀 0
⚠️ 0
No description
Updated Feb 17, 2021
JD2112/Alveolar-Cell-Type-Deconvolution
⭐ 1
🍴 1
👀 1
DNA methylome-based validation of induced sputum as an effective protocol to study lung immunity: construction of a classifier of pulmonary cell types
Updated May 2, 2024
JD2112/artic-pangolin-nf
Nextflow
pangolin wrapped in artic for both Illumina and Nanopore
Updated Mar 26, 2021
JD2112/atlas
Other
ATLAS - Three commands to start analyzing your metagenome data
Updated Mar 3, 2022
JD2112/awesome-genome-visualization
TypeScript
A list of interesting genome browser or genome-browser-like implementations
Updated Nov 6, 2022
JD2112/BCG-data-analysis
Updated Apr 15, 2025
JD2112/BIN20P001_AJH
Updated Mar 31, 2021
JD2112/bioinfo-docker-collection
A repository with recipies for packaging bioinformatics tools into docker images that are hosted on docker hub.
JD2112/Bioinformatics-Book
HTML
Everything in Bioinformatics
JD2112/Bioinformatics-for-microbiology
Updated Apr 25, 2023
JD2112/Bioinformatics-lecture
Bioinformatics for microbiology course lectures and other materials
Updated May 3, 2023
JD2112/bookverse
CSS
Updated Apr 19, 2024
JD2112/C19
Updated Mar 28, 2024
JD2112/CDIO2019
Python
JD2112/Cecilia-Analysis
JD2112/Cecret
Nextflow workflow for our analysis of SARS-COV-2
Updated Feb 22, 2021
JD2112/cell-type-deconv
Cell type deconvolution from DNA Methylation and Gene Expression data
Updated Sep 20, 2024
JD2112/cell-type-specific-CpGs
Updated Aug 18, 2020
JD2112/CellTypeAdjustment
Updated Jan 18, 2021
JD2112/cell_detection
Updated Sep 14, 2020
JD2112/CF-CGL-presentations
Updated Jan 13, 2025
JD2112/CF-manual
Bioinformatics Unit, Core Facility user manual
JD2112/CF-manual-personal
JavaScript
Updated Feb 18, 2025
JD2112/ChAMP
Updated Aug 23, 2021
JD2112/Claras-Analysis
Claras EPIC array analysis
JD2112/ClustScanR
Updated Dec 10, 2024
JD2112/Compare-GRanges
JD2112/ComplexPCA
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👀 2
a ggplot PCA with complex annotation
JD2112/cov-linage
Updated Jan 8, 2023
JD2112/DataScanR
Updated Jan 30, 2025
JD2112/DiffMethSeq
A NextFlow pipeline to perform differential methylation analysis from bismark-aligned files
Updated Jan 29, 2025
JD2112/DNAm
C
Human DNA methylation data analysis from Illumina arrays, sequencers, Nanopore, PacBio and Twist's custom panels
Updated Sep 19, 2023
JD2112/docker-sc2reporter
Dockerized version of the sc2reporter proggram.
Updated Mar 22, 2022
JD2112/eda-with-j
Exploratory Data Analysis from Clinical Data
JD2112/Epigenetics
Epigenetics paper R codes
Updated Aug 31, 2020
JD2112/EpiSmoker-MiinaOllikainen
Updated Sep 9, 2020
JD2112/exomeAnalysis
Shell
Updated Oct 8, 2020
JD2112/FFTrees_Philips
Updated Aug 21, 2020
JD2112/git-essentials
Essential docs to add any Git repos
Updated Apr 21, 2025
JD2112/gms-artic
A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019
Updated Mar 2, 2022
JD2112/gms-artic-private
Updated Oct 25, 2021
JD2112/gms-artic-test
Updated Dec 16, 2021
JD2112/gms-JASEN
Updated Jan 21, 2021
JD2112/gms-nallo
An analysis pipeline for long-reads from both PacBio and Oxford Nanopore Technologies (ONT), written in Nextflow.
Updated Apr 22, 2025
JD2112/GOanalysis
Updated Aug 19, 2021
JD2112/grape-RNAseq-nf
Updated Jan 26, 2021
JD2112/habijabi
Whatever comes in mind
Updated Apr 14, 2025
JD2112/illumina450k-filtering
A collection of resources to filter 'bad' probes from the Illumina 450k and EPIC methylation arrays
JD2112/IlluminaFiltering
Updated Aug 19, 2020
JD2112/Image-Processing-MATLAB
MATLAB
Acquired time lapse images from the IncuCyte® and processed with MATLAB to create a time-lapse video of one particular aggregate of bacteria
JD2112/InteractivePlots
Updated Jan 22, 2021
JD2112/JASEN
Epitypification pipeline for clinical NGS data. Written in NextFlow, Python & Bash.
Updated Aug 16, 2024
JD2112/JD2112
My personal repository
JD2112/jupyter-books
Updated Mar 7, 2022
JD2112/jyotirmoy-library
PHP
Updated Mar 16, 2025
JD2112/jyotirmoy-website
My personal website
JD2112/JyotirmoyCV
TeX
Updated Oct 29, 2024
JD2112/Lima2018
Updated Mar 29, 2021
JD2112/Lima2019
Lima 2019 data analysis and Figures
Updated Jul 20, 2021
JD2112/longqc.nf
Dockerfile
LongQC is a tool for the data quality control of the PacBio and ONT long reads.
JD2112/m2r
Markdown to reStructuredText converter
Updated Mar 9, 2022
JD2112/MachineLearning
JD2112/megalodon
Megalodon is a research command line tool to extract high accuracy modified base and sequence variant calls from raw nanopore reads by anchoring the information rich basecalling neural network output to a reference genome/transriptome.
Updated Mar 28, 2022
JD2112/metagen
metagenome, pangenome, and metabarcoding data analysis
JD2112/MethAna-book
Updated Nov 4, 2022
JD2112/methNext
A NextFlow pipeline to analyse DNA methylation data from different sequencing platforms, Illumina, Twist, Nanopore, PacBio
JD2112/methylr
⭐ 12
👀 12
⚠️ 3
methylR: a single shiny solution from sequencer data to pathway analysis
Updated Feb 9, 2025
JD2112/methylr-devel
all github repos and codes for DNA methylation analysis
Updated Sep 11, 2022
JD2112/methylr-registration-form
User registration form to use methylR application on the web server
Updated Oct 16, 2024
JD2112/methylr-shiny
⚠️ 11
JD2112/methylr2
Updated Sep 6, 2023
JD2112/My-eBook-Library
A shiny-based SQL database for book record keeping
JD2112/Mykrobe-tb-workflow
A workflow for analysis and resistance profiling of Mycobacterium tuberculosis nanopore data with Mykrobe
JD2112/mysite
Updated Oct 13, 2022
JD2112/NanoMeth
Methylation data analysis of Nanopore sequencing data
Updated Oct 13, 2023
JD2112/NetworkAnalysis-Studying
Updated Jun 20, 2021
JD2112/NetworkR
Updated May 4, 2021
JD2112/NextOmics
A NextFlow pipeline to analyse multi-omics data
JD2112/nextstrain-auspice
JD2112/nf-hack17-tutorial
Nextflow basic tutorial for newbie users
JD2112/nfcore-rnaseq
JD2112/pango-designation
Repository for suggesting new lineages that should be added to the current scheme
Updated May 6, 2021
JD2112/pangolin
Software package for assigning SARS-CoV-2 genome sequences to global lineages.
Updated Feb 23, 2021
JD2112/pangolin-nf
nextflow wrap up of pangolin
Updated Feb 24, 2021
JD2112/pathview
pathway based data integration and visualization
Updated Aug 28, 2021
JD2112/Pathway-Enrichment
JD2112/PathwayMap
Updated Nov 2, 2021
JD2112/pb-CpG-tools
Collection of tools for the analysis of CpG data
Updated May 14, 2022
JD2112/php-login-app
Create a login and registration form using PHP and MYSQLdb for ADMIN and USERs
Updated Feb 26, 2025
JD2112/Programming-Assignment-2
JD2112/Programs
Updated May 12, 2020
JD2112/Promptomics
The study and engineering of biological question-answering using LLMs.
JD2112/pythonVCF
python codes to analyze and sort VCF annotation file
JD2112/R-NextFlow
Creating R codes to run with nextflow
Updated Jul 21, 2021
JD2112/Rcode
Updated Mar 13, 2020
JD2112/Rcodes
Updated Mar 10, 2020
JD2112/reactCV
Java
Updated Feb 19, 2024
JD2112/RNAseq-Analysis
SCSS
RNAseq data analysis from Count and Fastq files
JD2112/rnaseq_nfcore
JD2112/rocker
R configurations for Docker
JD2112/RRBS-scripts-R
JD2112/RRBSscript
Single script analysis of RRBS data from RAW file to methylation information
Updated Jun 18, 2020
JD2112/RWorkshop
Updated Aug 27, 2019
JD2112/SBGNview
JD2112/scout
VCF visualization interface
Updated Nov 1, 2021
JD2112/script-tag-example
Component example with script tags for integration with other frameworks / existing applications
JD2112/scRNAseqR
JD2112/seurat-satijalab
Updated Aug 27, 2020
JD2112/shiny-conda-docker
JD2112/Shiny-Record-Keeper
JD2112/Shiny-WGCNA
Shiny app for WGCNA for RNAseq and DNA methylation data
JD2112/shinyCV
shiny application to create a CV
Updated Dec 18, 2022
JD2112/shinyepico
shinyÉPICo is a graphical and interactive pipeline to analyze Illumina DNA Methylation Arrays and to find Differentially Methylated CpGs
JD2112/ShinyOlink
A Shiny interface to analyse Olink data
Updated Mar 29, 2025
JD2112/shinyproxy-docker
JD2112/SIMDA
Single Individual Methylation Data Analysis (SIMDA) is a method to find the differential methylation analysis in a single participant's data having two different conditions.
JD2112/sproject
Updated Jun 27, 2024
JD2112/statina
JD2112/StatisticsWithR
JD2112/TBpatent
Updated Jan 28, 2021
JD2112/testing
Singularity
Updated Oct 22, 2021
JD2112/transcriptr
⚠️ 5
JD2112/TranscriptR-main
Updated Jan 11, 2024
JD2112/transcriptr-shiny
JD2112/tuberculosis-analysis
JD2112/TwistMethNext
A NextFlow pipeline for Twist NGS DNA Methylation data analysis
Updated Apr 8, 2025
JD2112/TwistMethNext-pro
Perl
JD2112/umap-tkonopka
JD2112/Unsupervised-Analysis-With-R
Illumina Infinium 450K BeadChip Array Analysis
JD2112/uwot-jlmelville
JD2112/validate-meta
Updated Sep 23, 2021
JD2112/webr
This project aims to compile the statistical language R into WASM for use in a browser, via Emscripten.
Updated Mar 23, 2023
JD2112/wordcloud
Updated May 27, 2020
JD2112/YAMP
YAMP: Yet Another Metagenomic Pipeline
Updated Dec 17, 2021