Biology & Genomics

Select restriction enzymes for cloning by cut frequency, overhangs and methylation

Predict restriction digest fragment sizes and compare them to gel patterns

Design and check Golden Gate assemblies for internal sites and overhang fidelity

Build restriction maps with cut positions and inter-site distances for plasmids

Find restriction enzyme cut sites in DNA sequences with Biopython

Plan retrosynthetic routes with AiZynthFinder and route scoring

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

Map translation start sites including non-AUG starts from TI-seq ribosome profiling

Detect translated ORFs from Ribo-seq using 3-nucleotide periodicity

Preprocess ribosome profiling reads with UMI handling and rRNA depletion

Check Ribo-seq library quality with 3-nucleotide periodicity and P-site offsets

Detect ribosome stalling and pausing at codon resolution from Ribo-seq

Quantify translation efficiency and test differential translation between conditions

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

View, convert and read SAM, BAM and CRAM alignment files with samtools and pysam

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

Analyze compound libraries by Murcko scaffolds, R-groups and matched pairs

Create and edit Biopython Seq, MutableSeq and SeqRecord objects

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

Slice sequences and concatenate exons into transcripts with Biopython

Calculate N50, auN, GC content and length statistics for sequence sets

Search compounds by 3D shape and electrostatic similarity with ROCS and USRCAT

Find similar molecules with Tanimoto, Tversky and Dice on fingerprints

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