Bioconductor Topics

Software infrastructure for efficient representation of full genomes and their SNPs

Forge your own BSgenome data package

Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data

Efficient manipulation of biological strings

Design of guide RNAs in CRISPR genome-editing systems

ChIPanalyser: Predicting Transcription Factor Binding Sites

DiffLogo: A comparative visualisation of biooligomer motifs

Identification and Annotation of Protein Hotspot Residues

Query the EDIR Database For Specific Gene

Introduce *Ranges to bedtools users

Interlog protein network reconstruction by Mapping and Mining ANalysis

KinSwingR: network-based kinase activity prediction

DNA IP-seq data analysis

Perform Methylation Analysis on Next Generation Sequencing Data

Detect binding sites from motifs and ChIP-seq experiments, and compare binding sites across conditions

Benchmarking Epigenomic Profiling Methods Using Motif Enrichment

PWM enrichment analysis

Quasispecies Diversity

Analysis of high-throughput sequencing data processed by restriction enzyme digestion

Inference on agreement between ordered lists

Mapping, quantification and variant analysis of sequencing data

Find SNV/Indel differences between two bam files with near relationship

NGS Read Simulator for FFPE Tissue

Implementation of the dot bracket annotations with Biostrings

SynMut: Designing Synonymously Mutated Sequences with Different Genomic Signatures

TVTB: The VCF Tool Box

Fast Sequence Mapping in High-Throughput shRNA and CRISPR Screens

Efficient manipulation of CIGAR strings

dagLogo: a Bioconductor package for visualizing conserved amino acid sequence pattern in groups based on probability theory

hapFabia: Identification of very short segments of identity by descent (IBD) characterized by rare variants in large sequencing data

Flexible Heatmaps for Functional Genomics and Sequence Features

IPD IMGT/HLA and IPD KIR database for Homo sapiens

motif matching, comparison, and de novo discovery using the MEME Suite

Data and functions for dealing with microRNAs

Plot stacked logos for single or multiple DNA, RNA and amino acid sequence

Perform key tests for binding motifs in sequence data

Multiple Sequence Alignment with MUSCLE

de novo Annotation of Pack-TYPE Transposable Elements

Set of tools to identify periodic occurrences of k-mers in DNA sequences

Positional combinatorial sequence demultiplexer

Identification of potential quadruplex forming sequences

Perform pairwise sequence alignments

Quantify the Extent of Evolutionary Evidence in Molecular Sequences

R Interface for the Basic Local Alignment Search Tool

Design Degenerate Oligos from a Multiple DNA Sequence Alignment

Pipeline for single cell multi-omic data pre-processing

scanMiR

scanMiR shiny application

Simulate Codons with Darwinian Selection Modelled as an OU Process

Sequence logos for DNA sequence alignments