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🛠️ Newbe

Open-source bioinformatics toolbox for researchers — 275+ interactive tools, ready to use

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🌟 What is Newbe?

Newbe is an open-source toolkit for bioinformatics researchers, providing 275+ interactive micro-tools covering everything from sequencing QC to publication-grade figures.

Each tool is standalone — no complex dependencies, just run the script and follow the prompts. All parameters have sensible defaults, press Enter to use them.

✨ Key Features

• 🎯 Interactive Input — Every parameter has prompts and defaults, press Enter to use defaults
• 📦 Standalone — Each tool is self-contained, no cross-tool dependencies
• 🐍 Dual Language — 190+ Python tools, 80+ R tools
• 🧬 Full Pipeline — From raw sequencing data to publication-grade figures
• 🔓 Open Source — MIT license, use/modify/share freely

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🚀 Quick Start

# 1. Clone the repository
git clone https://github.com/Elephenman/newbe.git
cd newbe

# 2. Navigate to a tool (e.g. sequencing QC)
cd sequencing-qc/fastq-qc-checker

# 3. Run
python fastq_qc_checker.py      # Python tool
Rscript seurat_qc_pipeline.R    # R tool

All tools use unified interactive input — each parameter has prompts and sensible defaults, press Enter to accept.

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📋 Tool Directory

Click a category to see detailed tool descriptions within that category.

🧬 Sequencing QC 18 FASTQ/BAM quality control, filtering, trimming, deduplication, sampling Adapter detection & trimming · Base quality distribution · Barcode splitting Duplicate read removal · Quality/length/GC filtering · Paired-end sync check Read length filtering · Strand orientation detection · UMI dedup statistics QC report aggregation · Sequencing depth calculation · Sample sheet validation	🔗 Alignment & BAM 8 BAM/SAM statistics, filtering, coverage, insert size Chromosome info extraction · Coverage distribution plot · SAM flag filtering Insert size statistics · Mate-pair resolution · Read count summarization BAM key metrics report · Coverage depth statistics
🧪 Variant & Genomic Analysis 28 VCF · SNP · CNV · SV · GWAS · Haplotype · Mutational Signature Manhattan & QQ plots · LD decay curve · Haplotype phasing (PS/HP tags) SBS96 signature extraction · CNV segment annotation · SV breakpoint visualization Germline/somatic variant filtering · Clinical annotation · Ancestry inference VCF filtering/parsing/concordance · MAF distribution · Missingness check	📊 RNA-seq & Expression 34 DESeq2 · DEG · Normalization · Volcano · Heatmap · WGCNA DESeq2 result formatting · Multi-group DEG comparison (Venn/UpSet) Volcano plot (interactive/enhanced/label editor) · Clustered heatmap TPM/FPKM/RPKM normalization · ERCC spike-in · Z-score transformation DEG effect size/FDR correction/meta-analysis · Batch effect inspection Expression boxplot/violin/percentile ranking · Splice junction counting
🔬 Single-Cell Analysis 36 Seurat · Annotation · Clustering · Integration · Pseudotime · CellChat Seurat QC pipeline & integration · Auto annotation · Marker gene discovery PCA/t-SNE/UMAP · Harmony batch correction · Batch UMAP coloring Pseudotime (Monocle3) · RNA velocity · Doublet detection & visualization Cell cycle scoring & regression · Variable feature selection · JackStraw test Cell proportion analysis · Neighborhood enrichment · Gene module & trend	🗺️ Spatial Transcriptomics 13 Spot annotation · DEG · Deconvolution · Moran · Niche · Neighbor graph Spot auto annotation & quality filtering · Spatial DEG discovery Deconvolution (SPOTlight) · Moran's I autocorrelation · Geary's test Niche detection · Neighbor graph construction · Zone boundary segmentation Co-expression map · Distance decay · Variability mapping
🧫 Epigenomics 14 ChIP-seq · ATAC-seq · Methylation · Hi-C · TF · Enhancer ATAC peak annotation · ChIP peak merging · Chromatin state annotation Methylation beta value · TF footprint detection · Motif scanning & enrichment Enhancer signal quantification & target linking · Hi-C contact matrix CTCF insulator boundary · Replication origin/timing · TF binding site comparison	📖 Genome Annotation 14 GTF · BED · Coordinate conversion · Promoter · Intron · Circos GTF exon/intron/feature extraction · BED intersection/merge/annotation Genome coordinate conversion (hg19↔hg38) · Promoter extraction Circos plot · Genome density plot · Multi-track overlay Repeat region masking · Genome bin statistics · Coverage interpolation
🧬 Sequence Analysis 15 FASTA · Alignment · k-mer · Codon · N50 · Synteny · Phylogenetics FASTA stats/reverse/slice · Needleman-Wunsch alignment · K-mer frequency Codon usage bias (RSCU/CAI) · N50/L50 statistics · Genome size estimation GC sliding window · Synteny block detection · Multi-FASTA concatenation Phylogenetic tree batch processing · Contig length distribution	🌐 Gene Function & Pathway 21 Enrichment · GSEA · Pathway network · DDR · Co-expression · WGCNA GO/KEGG enrichment pipeline · GSEA runner & rank file generation WGCNA module extraction · Co-expression network · Pathway cross-talk DDR pathway mapping/mutational scoring/damage hotspot/signal correlation Gene desert · Ortholog finder · Protein domain · Survival correlation Sankey flow diagram · Pathway heatmap/network · Multi-omics integration
🎨 Visualization & Plotting 18 Palette · Heatmap · Venn · Forest · Ridgeline · Dot plot Nature/Cell color palettes · Colorblind-safe palette · R plot template library Venn diagram (2-5 sets) · Forest plot · Ridgeline plot Heatmap annotation & sorting · Enhanced dot plot · Stacked bar chart Correlation matrix · Stats summary table · Boxplot outlier detection · Comparison table	🔄 Data Format Conversion 7 CSV↔TSV↔JSON↔Excel · ID mapping · FASTQ↔FASTA · SAM↔FASTQ Universal format conversion · DPI conversion (300/600) · FASTQ→FASTA GFF3→GTF · SAM/BAM→FASTQ · Gene ID version normalization Transcript ↔ Gene ID ↔ Gene name mapping
📋 Lab & Project Management 20 Environment · Init · Logs · Gantt · Reagents · Protocol Conda env check & export · Project directory init · Pipeline documentation Pipeline log parsing · Gantt chart + milestones · Protocol versioning Reagent inventory + expiry alerts · Experiment timer · Meeting minutes Grant budget calculator · Experiment design checker · Result aggregation · R template	📝 Academic Writing & Literature 29 PubMed · DOI · Citation · Notes · Manuscript · Conference · Grant PubMed batch search · DOI→citation format · Citation tracking & trends Obsidian note template · arXiv downloader · BibTeX network Deep paper reading · Readability score · Word/section count Figure compliance check/layout/labels · Reference cleanup · Conference abstract Thesis outline · Grant budget · Keyword extraction · Plagiarism check

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🧬 5 Original Sub-Projects

Phylogenetic tree batch processing 3 Python scripts

R scientific plot template library 106 plots + 51 SCI

Deep paper reading Reproducer + reviewer

Meeting pipeline Paper → PPT → defense

Obsidian↔Jupyter bidirectional sync MD ↔ IPYNB

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📄 License

MIT License — use freely, modify freely, share freely.