Biology & Genomics

Find genes with dynamic expression over time using splines and maSigPro

Detect differential alternative splicing between conditions with rMATS

Date outbreak phylogenies and estimate evolutionary rates with TreeTime and BEAST2

Read FASTQ quality scores and trim low quality bases with Biopython

Filter sequence records by length, ID, GC content or pattern with Biopython

Correct instrument drift in CyTOF and flow data with bead normalization

Find cell populations in cytometry data without gates using FlowSOM and PhenoGraph

Correct fluorophore spillover and transform flow cytometry data for analysis

Check flow and CyTOF acquisition quality for drift, flow rate and dead cells

Test cell population and marker changes between cytometry groups

Remove cell doublets from flow and mass cytometry data before analysis

Load and inspect Flow Cytometry Standard FCS files and their parameters

Define cell populations with rectangular, polygon and data driven gates

Convert sequence files between FASTA, FASTQ, GenBank and EMBL with Biopython

Call germline SNPs and indels with GATK HaplotypeCaller and VQSR filtering

Design cytosine and adenine base editing guides with editing window scoring

Design and score guide RNAs for Cas9 and Cas12a knockout or repression

Design ssODN and plasmid donor templates with optimized homology arms

Predict genome wide CRISPR off target sites and score guide specificity

Design pegRNAs with spacer, PBS and RT template for prime editing

Detect A and B chromatin compartments from Hi-C matrices with cooltools

Process Hi-C read pairs with pairtools, filter duplicates and classify contacts

Load, convert and export Hi-C contact matrices in cooler format

Find differential chromatin contacts between Hi-C conditions with fold changes

Draw Hi-C triangle plots, virtual 4C and multi track genome figures

Detect chromatin loops and enhancer promoter contacts from Hi-C data

Balance Hi-C matrices with ICE and compute observed over expected maps

Call topologically associating domains and boundaries from Hi-C insulation scores

Segment nuclei and whole cells in multiplexed tissue images with Cellpose or Mesmer

Load IMC MCD files and clean hot pixels before segmentation

Annotate cell types interactively in napari to train imaging classifiers

Assign cell types to segmented imaging mass cytometry cells from marker expression

Check imaging mass cytometry signal to noise and acquisition quality

Test cell neighborhood enrichment and interactions in imaging mass cytometry data

Predict B cell and T cell epitopes in antigens for vaccine and antibody design

Predict peptide binding to MHC class I and II with MHCflurry and NetMHCpan

Match T cell receptors to their cognate epitopes with deep learning models

Find isoform switches and their effects on protein domains and NMD sensitivity

Call SNPs and small indels from Nanopore or PacBio reads with Clair3

Discover and quantify full length isoforms from PacBio Iso-Seq data

Call 5mC and 6mA methylation directly from Nanopore signal without bisulfite

Align Nanopore and PacBio long reads to a reference with minimap2 presets

Polish Nanopore assemblies and call variants with medaka neural networks

Assess and filter long read runs with NanoPlot, NanoStat and chopper

Detect structural variants from long read alignments with Sniffles and cuteSV

Identify and quantify lipid classes from LC-MS data with MS-DIAL and LipidMaps

Identify metabolites from m/z and retention time with MS/MS spectral matching

Preprocess metabolomics data with MS-DIAL peak detection and alignment

Correct metabolomics batch effects and normalize data using QC samples