Tagged bioinformatics

Quantify base and prime editing outcomes, bystander edits and indel rates

Correct batch effects when combining pooled CRISPR screens across batches

Measure indel and HDR editing efficiency from amplicon sequencing with CRISPResso2

Call essential and resistance genes from CRISPR screen counts with MAGeCK and BAGEL2

Model sgRNA efficacy and gene essentiality across several CRISPR knockout screens

Design custom sgRNA libraries with selection, controls and oligo ordering

Rank genes in pooled CRISPR knockout screens with MAGeCK count analysis

Check library representation and replicate correlation before calling hits

Detect tumor mutations in plasma DNA at low allele fractions using UMIs

Run differential expression on RNA-seq counts with DESeq2 in R

Run differential expression on RNA-seq counts with edgeR and quasi likelihood tests

Remove batch effects from RNA-seq expression with ComBat and SVA

Find genes with dynamic expression over time using splines and maSigPro

Screen bacterial genomes for antimicrobial resistance genes with AMRFinderPlus

Type bacterial isolates with MLST and core genome MLST to track outbreak clones

Date outbreak phylogenies and estimate evolutionary rates with TreeTime and BEAST2

Infer who infected whom in an outbreak from genomic and case data

Assign viral lineages with Nextclade and pangolin to track variants of concern

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

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

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

Detect antimicrobial resistance genes in isolates and metagenomes

Profile species level relative abundances with MetaPhlAn 4 marker genes

Align bisulfite sequencing reads to a reference with Bismark and bowtie2

Analyze DNA methylation from Bismark coverage files with methylKit in R

Run Gene Ontology over representation tests on gene lists with clusterProfiler

Run gene set enrichment on ranked gene lists with clusterProfiler GSEA

Find KEGG pathways and modules enriched in a gene list across many organisms

Test gene lists against Reactome pathways with over representation and GSEA

Run WikiPathways enrichment and GSEA on gene lists for 30 plus species

Measure distances, angles, RMSD and surface area on protein structures

Read, write and download protein structures in PDB and mmCIF formats

Edit protein structures by moving atoms, removing residues or changing B factors

Navigate protein structure models, chains and residues with Biopython

Load mzML and MaxQuant proteinGroups files and filter contaminant proteins

Find proteins that change abundance between groups with limma or MSstats

Resolve shared peptides into protein groups with protein level FDR control

Quantify proteins from label free, TMT and SILAC mass spectrometry data

Screen sequencing reads for cross species and sample swap contamination

Generate and read FastQC and MultiQC reports for raw sequencing data

Check RNA-seq libraries for rRNA contamination, strandedness and coverage bias