Community — IndianElucidBiology | Ask Questions, Share Results, Learn Together

General Channels

Start here when you join

#welcome-and-rules

Server rules, how to ask good questions, and links to resources. Read before posting.

📌 Pinned

#introductions

Introduce yourself — your background, what you're working on, and what you hope to learn.

👋 New members

#general-bioinformatics

Open discussion — tools, papers, career advice, software recommendations, and anything bioinformatics.

💬 Active

#show-your-work

Share your completed analyses, plots, and results. Celebrate your wins and get feedback from the community.

🏆 Showcase

#resources-and-papers

Share useful papers, datasets, tools, databases, and learning materials with the community.

📚 Resources

#jobs-and-opportunities

PhD positions, postdocs, internships, and bioinformatics job postings. Also for CV/resume advice.

💼 Careers

Transcriptomics

RNA-Seq, scRNA-Seq, WGCNA, splicing

#rna-seq-help

Questions about bulk RNA-Seq — alignment (HISAT2, STAR), quantification (featureCounts, salmon), DESeq2, edgeR.

DESeq2 STAR

#single-cell-scrna

scRNA-Seq with Seurat, Scanpy, Cell Ranger. Clustering, trajectory, doublet detection, integration, cell type annotation.

Seurat Scanpy

#wgcna-coexpression

Co-expression networks using WGCNA, hdWGCNA, and related tools. Module-trait relationships, hub genes.

WGCNA

#splicing-and-isoforms

Differential splicing with rMATS, LeafCutter, SUPPA2. Long-read RNA-Seq with Minimap2 and NanoStat.

rMATS

#functional-enrichment

GO enrichment, GSEA, pathway analysis with clusterProfiler, KEGG, Reactome. Interpretation and visualisation.

clusterProfiler GSEA

Genomics

Variant calling, assembly, annotation, CNV

#variant-calling

GATK HaplotypeCaller, BCFtools, DeepVariant. GVCF, joint genotyping, VQSR, hard filtering. Short and long-read variants.

GATK BCFtools

#variant-annotation

SnpEff, SnpSift, VEP, ANNOVAR. Functional annotation, filtering by impact, ClinVar, dbSNP lookups.

SnpEff VEP

#genome-assembly

Hifiasm, Flye, SPAdes, Canu. Short vs long-read assembly, scaffolding with Hi-C, polishing with Medaka/Pilon.

Hifiasm Flye

#genome-annotation

MAKER, BRAKER2, Augustus, BUSCO quality assessment. Repeat masking with RepeatMasker and RepeatModeler.

MAKER BRAKER2

#cnv-and-sv

Copy number variation from WGS/WES. Structural variants with Delly, Lumpy, Manta. CNVnator, Control-FREEC.

CNV SV

#somatic-cancer-genomics

Somatic mutation calling with Mutect2, Strelka2. Tumour-normal pairs, mutational signatures, cancer driver analysis.

Mutect2

Population Genomics

GWAS, pop gen stats, linkage, QTL

#gwas-population-genetics

GWAS with PLINK, GEMMA, SAIGE. Population structure, kinship matrices, mixed models, Manhattan plots.

PLINK GEMMA

#fst-and-popgen-stats

Fst, π (nucleotide diversity), Tajima's D, XP-EHH selective sweeps. VCFtools, PopLDdecay, iHS.

VCFtools Fst

#haplotype-and-phasing

Haplotype phasing with SHAPEIT4, BEAGLE, WhatsHap. LD analysis, haploview, introgression with ABBA-BABA.

SHAPEIT4

#linkage-and-qtl

Linkage map construction with JoinMap, R/qtl2, ASMap. QTL interval mapping, composite interval mapping, multi-QTL models.

R/qtl2 JoinMap

#admixture-and-structure

Population structure with ADMIXTURE, STRUCTURE, fastSTRUCTURE, PCA. TreeMix migration graphs, EIGENSOFT.

ADMIXTURE

#demographic-history

PSMC, SMC++, MSMC for population size history. Coalescent simulations with msprime, SLiM.

PSMC msprime

Phylogenetics & Comparative Genomics

Trees, synteny, orthology, selection

#phylogenetics

IQ-TREE, RAxML, MrBayes, BEAST. Model selection, bootstrap, concordance factors, time-calibrated trees.

IQ-TREE RAxML

#comparative-genomics

Synteny with MCScanX, MUMmer, SyRI. Orthology with OrthoFinder, OrthoMCL. Gene family evolution.

OrthoFinder MCScanX

#positive-selection

dN/dS with PAML codeml, HyPhy. Branch-site models, RELAX, FEL/MEME for episodic selection.

PAML HyPhy

#wgd-and-polyploidy

Whole genome duplication analysis, polyploidy, Ks distributions, subgenome phasing, WGDdetector.

Ks plots

Epigenomics & Multi-omics

ATAC-seq, ChIP-seq, methylation, proteomics

#atac-seq-chip-seq

Peak calling with MACS2/3, HOMER. ATACseqQC, ChIPseeker, motif analysis, differential accessibility.

MACS2 HOMER

#methylation-analysis

Bismark for WGBS, differential methylation with DSS, methylKit. CpG islands, DMRs, methylation heatmaps.

Bismark DSS

#proteomics

MaxQuant, Perseus, MSFragger for mass spectrometry proteomics. LFQ normalisation, volcano plots, protein networks.

MaxQuant Perseus

Metagenomics & Microbiome

QIIME2, Kraken2, MAGs, diversity

#qiime2-amplicon

16S/ITS amplicon sequencing with QIIME2. DADA2, taxonomy assignment, alpha/beta diversity, PCoA plots.

QIIME2 DADA2

#shotgun-metagenomics

Kraken2, Bracken taxonomic profiling. MetaPhlAn4, HUMAnN3. Functional profiling and community composition.

Kraken2 MetaPhlAn

#mags-and-binning

Metagenome-assembled genomes with MetaBAT2, MaxBin, CONCOCT. CheckM quality, GTDB-Tk taxonomy.

MetaBAT2 CheckM

Tools, Coding & HPC

R, Python, Linux, Snakemake, containers

#r-programming

ggplot2, Bioconductor, tidyverse, data wrangling. Package installation issues, StackOverflow-style R help.

R ggplot2

#python-for-bioinformatics

Biopython, Pandas, Scanpy, scikit-learn. Jupyter notebooks, scripting pipelines, parsing FASTA/VCF/GFF.

Python Biopython

#linux-and-hpc

Bash, SLURM, PBS, conda/mamba environments. SSH, file transfer, cluster job arrays, shell scripting tips.

Linux SLURM

#snakemake-and-nextflow

Workflow management with Snakemake and Nextflow/nf-core. DAG construction, cloud execution, reproducibility.

Snakemake Nextflow

#docker-and-singularity

Containerised bioinformatics — Docker, Singularity/Apptainer, Conda environments, reproducible research.

Docker Conda

Community Rules

Be kind and respectful. No harassment, discrimination, or toxic behaviour. Everyone is learning.

Post in the right channel. RNA-Seq questions in #rna-seq-help, GWAS in #gwas-population-genetics, etc.

Share your error message and code. "It doesn't work" is not enough. Paste the exact error and what you tried.

No spam, self-promotion, or off-topic links. Use #resources-and-papers for sharing tools and papers.

Mark questions resolved. Reply with ✅ when your issue is solved so others can find the answer later.

FAQ

Is this community completely free?

Yes, 100% free forever. Discord is free, and this server will never have paid tiers or paywalled channels. All tutorials on IndianElucidBiology are also free.

I'm a complete beginner — is this community for me?

Absolutely. Start with the #welcome-and-rules channel, introduce yourself in #introductions, and then head to the Bioinformatics 101 tutorial. Ask any question — no question is too basic.

How do I ask a good bioinformatics question?

Share: (1) What you're trying to do, (2) The exact command you ran, (3) The exact error message, (4) Your OS, tool version, and input data format. The more context you give, the faster you'll get a useful answer.

Can I share my own tutorials or scripts?

Yes! Post scripts in #show-your-work and tutorials/resources in #resources-and-papers. We encourage community contributions.

What if my question isn't answered?

Be patient — the community is growing. You can also email mr.ank2999@gmail.com for direct help from Ankush.

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