Biocview "Alignment"

A graphical interface for the metagene package
A graphical interface for the metagene package
Alignment of LC-MS Profiles by Neighbor-wise Compound-specific Graphical Time Warping with Misalignment Detection
Alignment of LC-MS Profiles by Neighbor-wise Compound-specific Graphical Time Warping with Misalignment Detection
Analysis of alternative splicing using RNA-Seq
Analysis of alternative splicing using RNA-Seq
Analysis of alternative splicing using RNA-Seq
Analyze high-throughput sequencing of T and B cell receptors
Analyze high-throughput sequencing of T and B cell receptors
An Easy-to-use Systematic pipeline for ATACseq data analysis
An Easy-to-use Systematic pipeline for ATACseq data analysis
An Easy-to-use Systematic pipeline for ATACseq data analysis
An Easy-to-use Systematic pipeline for ATACseq data analysis
An Easy-to-use Systematic pipeline for ATACseq data analysis
A normalization and copy number estimation method for single-cell DNA sequencing
A normalization and copy number estimation method for single-cell DNA sequencing
An R interface to the GMAP/GSNAP/GSTRUCT suite
An R package for RNA visualization and analysis
An R package for the creation of complex genomic profile plots
an R package for visualization of tree and annotation data
an R package for visualization of tree and annotation data
an R package for visualization of tree and annotation data
An R Wrapper for Bowtie2 and AdapterRemoval
A package to produce metagene plots
A package to produce metagene plots
A package to produce metagene plots
Automated analysis of CRISPR experiments
Automated analysis of CRISPR experiments
BadRegionFinder: an R/Bioconductor package for identifying regions with bad coverage
Base Classes and Functions for Phylogenetic Tree Input and Output
Base Classes and Functions for Phylogenetic Tree Input and Output
Base Classes and Functions for Phylogenetic Tree Input and Output
Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data
BBCAnalyzer: an R/Bioconductor package for visualizing base counts
Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
Bioinformatics pipelines based on Rcwl
Bioinformatics pipelines based on Rcwl
Calculate strandness information of a bam file
Calculate strandness information of a bam file
Calculate strandness information of a bam file
ChIPanalyser: Predicting Transcription Factor Binding Sites
ChIPanalyser: Predicting Transcription Factor Binding Sites
ChIPanalyser: Predicting Transcription Factor Binding Sites
ChIPexoQual
ChIPexoQual
ChIPUtils - A package to perform exploratory analysis of ChIP data and most commonly used QC measures
Cut rDNA Sequences Into Domains Using Covariance Models
DegNorm: degradation normalization for RNA-seq data
Detection of site fixation in molecular evolution
Detection of site fixation in molecular evolution
Detection of sites with fixation of amino acid substitutions in protein evolution
Differential Analyis of Hi-C Data
Differential Analysis of Hi-C Data
DiffLogo: A comparative visualisation of biooligomer motifs
DiffLogo: A comparative visualisation of biooligomer motifs
Dynamic Programming Based Alignment of MS2 Chromatograms
Dynamic Programming Based Alignment of MS2 Chromatograms
Dynamic Programming Based Alignment of MS2 Chromatograms
Dynamic Programming Based Alignment of MS2 Chromatograms
Dynamic Programming Based Alignment of MS2 Chromatograms
EDLogo Plots Featuring String Logos and Adaptive Scaling of Position-Weight Matrices
EDLogo Plots Featuring String Logos and Adaptive Scaling of Position-Weight Matrices
Efficient manipulation of biological strings
Efficient manipulation of biological strings
Efficient manipulation of biological strings
Extract read count signals from bam files
Extract read count signals from bam files
Fast Sequence Mapping in High-Throughput shRNA and CRISPR Screens
Find SNV/Indel differences between two bam files with near relationship
Functionality Visualization for Motifs
Functions to creation of low dimensional comparative matrices of Amino Acid Sequence occurrences
Functions to creation of low dimensional comparative matrices of Amino Acid Sequence occurrences
Functions to creation of low dimensional comparative matrices of Amino Acid Sequence occurrences
Generate synthetic nucleosome maps
Generate synthetic nucleosome maps
Gimpute: An efficient genetic data processing and imputation pipeline
Grey Lists -- Mask Artefact Regions Based on ChIP Inputs
Guitar
GWAS trait-associated SNP enrichment analyses in genomic intervals
Identification and Annotation of Protein Hotspot Residues
Identification and Annotation of Protein Hotspot Residues
Implementation of the dot bracket annotations with Biostrings
Implementation of the dot bracket annotations with Biostrings
Interactive Analysis of Single Cell RNA-Seq Data
Interactive Analysis of Single Cell RNA-Seq Data
Interactive Analysis of Single Cell RNA-Seq Data
Interface for Popular Multiple Sequence Alignment Tools
Interface to Call Programs from Infernal RNA Covariance Model Package
Interlog protein network reconstruction by Mapping and Mining ANalysis
Interlog protein network reconstruction by Mapping and Mining ANalysis
Intron-Exon Retention Estimator
Intron-Exon Retention Estimator
KnowSeq R/Bioc package: Beyond the traditional Transcriptomic pipeline
KnowSeq R/Bioc package: Beyond the traditional Transcriptomic pipeline
LowMACA - Low frequency Mutation Analysis via Consensus Alignment
LowMACA - Low frequency Mutation Analysis via Consensus Alignment
LowMACA - Low frequency Mutation Analysis via Consensus Alignment
Methods for identifying small RNA loci from high-throughput sequencing data
Methylation Analysis Based on Signal Detection
MethylIT utility
Multiple Sequence Alignment
Multiple Sequence Alignment Handling and Inspection
Multiple Sequence Alignment with MUSCLE
NGS Read Simulator for FFPE Tissue
NGS Read Simulator for FFPE Tissue
Normalization and difference calling in ChIP-seq data
Normalization and difference calling in ChIP-seq data
Open Reading Frames in Genomics
Open Reading Frames in Genomics
Open Reading Frames in Genomics
Outlier detection in multiple sequence alignments
OUTRIDER - OUTlier in RNA-Seq fInDER
OUTRIDER - OUTlier in RNA-Seq fInDER
Perform Methylation Analysis on Next Generation Sequencing Data
Plot stacked logos for single or multiple DNA, RNA and amino acid sequence
Plot stacked logos for single or multiple DNA, RNA and amino acid sequence
Prediction of Protein Conserved Regions Using NADDA Algorithm
Pre-processing PTR-TOF-MS Data
Quantify and Annotate Short Reads in R
Quantify and Annotate Short Reads in R
Quasispecies Diversity
Quasispecies Diversity
R bowtie wrapper
Representation and manipulation of short genomic alignments
Representation and manipulation of short genomic alignments
Ribosome Profiling Data Analysis: from BAM to Data Representation and Interpretation
RNASeqR: an R package for automated two-group RNA-Seq analysis workflow
RNASeqR: an R package for automated two-group RNA-Seq analysis workflow
RNASeqR: an R package for automated two-group RNA-Seq analysis workflow
R Wrapper for HISAT2 Aligner
samExploreR package: high-performance read summarisation to count vectors with avaliability of sequencing depth reduction simulation
samExploreR package: high-performance read summarisation to count vectors with avaliability of sequencing depth reduction simulation
sangeranalyseR: a suite of functions for the analysis of Sanger sequence data in R
Segvis: A package for visualization of high throughput sequencing data along genomic segments
SEQprocess : a modularized and customizable pipeline framework for NGS processing in R package.
Set of tools to analyze ATAC-seq data
Set of tools to identify periodic occurrences of k-mers in DNA sequences
Single Cell RNA-Seq UMI Filtering Facilitator (scruff)
Single Cell RNA-Seq UMI Filtering Facilitator (scruff)
Single Cell RNA-Seq UMI Filtering Facilitator (scruff)
Single Cell RNA-Seq UMI Filtering Facilitator (scruff)
Single Cell RNA-Seq UMI Filtering Facilitator (scruff)
Single Cell RNA-Seq UMI Filtering Facilitator (scruff)
Software Package for Transcription Factor Binding Site (TFBS) Analysis
Software Package for Transcription Factor Binding Site (TFBS) Analysis
Subread Sequence Alignment and Counting for R
Synteny Alignment and Analysis for Saccharomyces sensu stricto
systemPipeRdata: NGS workflow templates and sample data
systemPipeR: NGS workflow and report generation environment
systemPipeR: NGS workflow and report generation environment
TARgeted SEQuencing Experiment Quality Control
TARgeted SEQuencing Experiment Quality Control
Tools for curating, analyzing, and manipulating biological sequences
Transcriptome-guided quality assessment of m6A-seq data
Translational control assessment from ribosome footprint and total RNA libraries
TVTB: The VCF Tool Box
TVTB: The VCF Tool Box
UMI4Cats: Processing, analysis and visualization of UMI-4C chromatin contact data
uORF prediction in R
Visualization Tool for Sequence Recombination and Reassortment
Visualization Tool for Sequence Recombination and Reassortment
Visualization tools for gene fusions
Visualization tools for gene fusions