Tagged bioinformatics

Run RNA-seq post-alignment QC for strandedness, coverage bias and rRNA contamination

Collapse UMI reads to molecules with umi_tools and fgbio consensus calling

Detect distant protein homologs with profile and structure methods beyond BLAST

Find restriction enzyme cut sites in DNA sequences with Biopython

Generate reverse complements and minus-strand coordinates for DNA and RNA

Quantify transcripts from FASTQ without alignment using Salmon or kallisto

Check RNA-seq count matrices for library size, outliers and batch before DE

Count reads per gene from aligned BAM files with Subread featureCounts

Import Salmon and kallisto transcript counts into DESeq2 or edgeR with tximport

Test RNA secondary structures against evolutionary covariation with R-scape

Search for noncoding RNA homologs and families with Infernal covariance models

Predict RNA secondary structure ensembles with ViennaRNA and consensus folding

Turn SHAPE and DMS probing data into reactivity profiles for RNA folding

Plot RNA-seq coverage with splice junction counts as sashimi figures

Calculate GC skew, melting temperature, molecular weight and pI for sequences

Integrate multiple scRNA-seq batches with Harmony, scVI, Seurat and fastMNN

Annotate single-cell clusters with CellTypist, SingleR and Azimuth references

Infer ligand-receptor cell communication from scRNA-seq with LIANA and CellChat

Cluster single-cell RNA-seq data with Leiden or Louvain in Scanpy and Seurat

Separate malignant from normal cells and infer copy number in tumor scRNA-seq

Convert single-cell objects between AnnData, Seurat and SingleCellExperiment

Test cell type composition changes between conditions with Milo and scCODA

Detect and remove doublets from single-cell RNA-seq with scDblFinder and Scrublet

Assign pooled hashed cells to samples with HTO and MULTI-seq demultiplexing

Reconstruct single-cell lineage trees from CRISPR scars and barcodes

Find cluster marker genes and hand-label cell types in single-cell data

Infer metabolite-mediated cell communication from scRNA-seq with MEBOCOST

Integrate CITE-seq, Multiome and unpaired single-cell modalities with joint methods

Assign guides and test effects in Perturb-seq and CROP-seq single-cell screens

Filter low-quality cells and remove ambient RNA in single-cell data

Analyze single-cell ATAC-seq fragments with Signac, ArchR and SnapATAC2

Analyze alternative splicing in single cells and pick the right library chemistry

Infer developmental trajectories, pseudotime and RNA velocity from single-cell data

Test miRNAs for differential expression with DESeq2 or edgeR

Discover novel miRNAs from small RNA reads with miRDeep2 scoring

Quantify miRNAs and isomiRs fast with miRge3.0 against miRBase or MirGeneDB

Trim small RNA adapters and collapse miRNA and piRNA reads with cutadapt

Predict and rank miRNA target genes with seed-based and validated databases

Profile tRNA fragments, piRNAs and snoRNA-derived small RNAs with MINTmap

Build single-cell-like units from Visium HD and Stereo-seq spatial bins

Combine spatial RNA with protein or ATAC data in multiomic spatial experiments

Analyze CODEX, MIBI, IMC and CyCIF protein images as intensity data

Detect spatially variable genes and cell colocalization with Squidpy

Predict whether a DNA variant alters splicing with SpliceAI and Pangolin

Check RNA-seq quality for splicing analysis with junction saturation and design audits

Quantify percent spliced in from RNA-seq with rMATS, SUPPA2 and MAJIQ

Download raw sequencing reads from SRA and ENA with sra-tools

Detect ligand-binding pockets on apo protein structures with fpocket and P2Rank

Measure distances, angles, RMSD and SASA on protein structures with Bio.PDB