Showing 53 of total 53 results (show query)
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Biostrings:Efficient manipulation of biological strings
Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences.
Maintained by Hervé Pagès. Last updated 1 months ago.
sequencematchingalignmentsequencinggeneticsdataimportdatarepresentationinfrastructurebioconductor-packagecore-package
62 stars 17.77 score 8.6k scripts 1.2k dependentsbioc
BSgenome:Software infrastructure for efficient representation of full genomes and their SNPs
Infrastructure shared by all the Biostrings-based genome data packages.
Maintained by Hervé Pagès. Last updated 2 months ago.
geneticsinfrastructuredatarepresentationsequencematchingannotationsnpbioconductor-packagecore-package
9 stars 14.12 score 1.2k scripts 267 dependentsbioc
seqLogo:Sequence logos for DNA sequence alignments
seqLogo takes the position weight matrix of a DNA sequence motif and plots the corresponding sequence logo as introduced by Schneider and Stephens (1990).
Maintained by Robert Ivanek. Last updated 5 months ago.
4 stars 10.57 score 304 scripts 29 dependentsbioc
Rsubread:Mapping, quantification and variant analysis of sequencing data
Alignment, quantification and analysis of RNA sequencing data (including both bulk RNA-seq and scRNA-seq) and DNA sequenicng data (including ATAC-seq, ChIP-seq, WGS, WES etc). Includes functionality for read mapping, read counting, SNP calling, structural variant detection and gene fusion discovery. Can be applied to all major sequencing techologies and to both short and long sequence reads.
Maintained by Wei Shi. Last updated 9 days ago.
sequencingalignmentsequencematchingrnaseqchipseqsinglecellgeneexpressiongeneregulationgeneticsimmunooncologysnpgeneticvariabilitypreprocessingqualitycontrolgenomeannotationgenefusiondetectionindeldetectionvariantannotationvariantdetectionmultiplesequencealignmentzlib
9.24 score 892 scripts 10 dependentsbioc
scPipe:Pipeline for single cell multi-omic data pre-processing
A preprocessing pipeline for single cell RNA-seq/ATAC-seq data that starts from the fastq files and produces a feature count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols.
Maintained by Shian Su. Last updated 3 months ago.
immunooncologysoftwaresequencingrnaseqgeneexpressionsinglecellvisualizationsequencematchingpreprocessingqualitycontrolgenomeannotationdataimportcurlbzip2xz-utilszlibcpp
68 stars 9.02 score 84 scriptsbioc
memes:motif matching, comparison, and de novo discovery using the MEME Suite
A seamless interface to the MEME Suite family of tools for motif analysis. 'memes' provides data aware utilities for using GRanges objects as entrypoints to motif analysis, data structures for examining & editing motif lists, and novel data visualizations. 'memes' functions and data structures are amenable to both base R and tidyverse workflows.
Maintained by Spencer Nystrom. Last updated 5 months ago.
dataimportfunctionalgenomicsgeneregulationmotifannotationmotifdiscoverysequencematchingsoftware
50 stars 8.69 score 117 scripts 1 dependentsbioc
pwalign:Perform pairwise sequence alignments
The two main functions in the package are pairwiseAlignment() and stringDist(). The former solves (Needleman-Wunsch) global alignment, (Smith-Waterman) local alignment, and (ends-free) overlap alignment problems. The latter computes the Levenshtein edit distance or pairwise alignment score matrix for a set of strings.
Maintained by Hervé Pagès. Last updated 11 days ago.
alignmentsequencematchingsequencinggeneticsbioconductor-package
1 stars 8.48 score 27 scripts 104 dependentsbioc
rBLAST:R Interface for the Basic Local Alignment Search Tool
Seamlessly interfaces the Basic Local Alignment Search Tool (BLAST) running locally to search genetic sequence data bases. This work was partially supported by grant no. R21HG005912 from the National Human Genome Research Institute.
Maintained by Michael Hahsler. Last updated 3 months ago.
geneticssequencingsequencematchingalignmentdataimportbioconductorbioinformaticsblast-search
106 stars 8.07 score 106 scriptsbioc
motifStack:Plot stacked logos for single or multiple DNA, RNA and amino acid sequence
The motifStack package is designed for graphic representation of multiple motifs with different similarity scores. It works with both DNA/RNA sequence motif and amino acid sequence motif. In addition, it provides the flexibility for users to customize the graphic parameters such as the font type and symbol colors.
Maintained by Jianhong Ou. Last updated 3 months ago.
sequencematchingvisualizationsequencingmicroarrayalignmentchipchipchipseqmotifannotationdataimport
7.93 score 188 scripts 6 dependentsbioc
CRISPRseek:Design of guide RNAs in CRISPR genome-editing systems
The package encompasses functions to find potential guide RNAs for the CRISPR-based genome-editing systems including the Base Editors and the Prime Editors when supplied with target sequences as input. Users have the flexibility to filter resulting guide RNAs based on parameters such as the absence of restriction enzyme cut sites or the lack of paired guide RNAs. The package also facilitates genome-wide exploration for off-targets, offering features to score and rank off-targets, retrieve flanking sequences, and indicate whether the hits are located within exon regions. All detected guide RNAs are annotated with the cumulative scores of the top5 and topN off-targets together with the detailed information such as mismatch sites and restrictuion enzyme cut sites. The package also outputs INDELs and their frequencies for Cas9 targeted sites.
Maintained by Lihua Julie Zhu. Last updated 19 days ago.
immunooncologygeneregulationsequencematchingcrispr
7.18 score 51 scripts 2 dependentsbioc
DiffLogo:DiffLogo: A comparative visualisation of biooligomer motifs
DiffLogo is an easy-to-use tool to visualize motif differences.
Maintained by Hendrik Treutler. Last updated 5 months ago.
softwaresequencematchingmultiplecomparisonmotifannotationvisualizationalignment
8 stars 6.66 score 27 scriptsbioc
Structstrings:Implementation of the dot bracket annotations with Biostrings
The Structstrings package implements the widely used dot bracket annotation for storing base pairing information in structured RNA. Structstrings uses the infrastructure provided by the Biostrings package and derives the DotBracketString and related classes from the BString class. From these, base pair tables can be produced for in depth analysis. In addition, the loop indices of the base pairs can be retrieved as well. For better efficiency, information conversion is implemented in C, inspired to a large extend by the ViennaRNA package.
Maintained by Felix G.M. Ernst. Last updated 5 months ago.
dataimportdatarepresentationinfrastructuresequencingsoftwarealignmentsequencematchingbioconductorrnarna-structural-analysisrna-structuresequencesstructures
4 stars 6.46 score 3 scripts 4 dependentsbioc
scanMiR:scanMiR
A set of tools for working with miRNA affinity models (KdModels), efficiently scanning for miRNA binding sites, and predicting target repression. It supports scanning using miRNA seeds, full miRNA sequences (enabling 3' alignment) and KdModels, and includes the prediction of slicing and TDMD sites. Finally, it includes utility and plotting functions (e.g. for the visual representation of miRNA-target alignment).
Maintained by Pierre-Luc Germain. Last updated 5 months ago.
mirnasequencematchingalignment
5.89 score 52 scripts 1 dependentsbioc
TVTB:TVTB: The VCF Tool Box
The package provides S4 classes and methods to filter, summarise and visualise genetic variation data stored in VCF files. In particular, the package extends the FilterRules class (S4Vectors package) to define news classes of filter rules applicable to the various slots of VCF objects. Functionalities are integrated and demonstrated in a Shiny web-application, the Shiny Variant Explorer (tSVE).
Maintained by Kevin Rue-Albrecht. Last updated 5 months ago.
softwaregeneticsgeneticvariabilitygenomicvariationdatarepresentationguidnaseqwholegenomevisualizationmultiplecomparisondataimportvariantannotationsequencingcoveragealignmentsequencematching
2 stars 5.76 score 16 scriptsbioc
QSutils:Quasispecies Diversity
Set of utility functions for viral quasispecies analysis with NGS data. Most functions are equally useful for metagenomic studies. There are three main types: (1) data manipulation and exploration—functions useful for converting reads to haplotypes and frequencies, repairing reads, intersecting strand haplotypes, and visualizing haplotype alignments. (2) diversity indices—functions to compute diversity and entropy, in which incidence, abundance, and functional indices are considered. (3) data simulation—functions useful for generating random viral quasispecies data.
Maintained by Mercedes Guerrero-Murillo. Last updated 5 months ago.
softwaregeneticsdnaseqgeneticvariabilitysequencingalignmentsequencematchingdataimport
5.56 score 8 scripts 1 dependentsbioc
rprimer:Design Degenerate Oligos from a Multiple DNA Sequence Alignment
Functions, workflow, and a Shiny application for visualizing sequence conservation and designing degenerate primers, probes, and (RT)-(q/d)PCR assays from a multiple DNA sequence alignment. The results can be presented in data frame format and visualized as dashboard-like plots. For more information, please see the package vignette.
Maintained by Sofia Persson. Last updated 5 months ago.
alignmentddpcrcoveragemultiplesequencealignmentsequencematchingqpcr
4 stars 5.49 score 13 scriptsbioc
MotifPeeker:Benchmarking Epigenomic Profiling Methods Using Motif Enrichment
MotifPeeker is used to compare and analyse datasets from epigenomic profiling methods with motif enrichment as the key benchmark. The package outputs an HTML report consisting of three sections: (1. General Metrics) Overview of peaks-related general metrics for the datasets (FRiP scores, peak widths and motif-summit distances). (2. Known Motif Enrichment Analysis) Statistics for the frequency of user-provided motifs enriched in the datasets. (3. De-Novo Motif Enrichment Analysis) Statistics for the frequency of de-novo discovered motifs enriched in the datasets and compared with known motifs.
Maintained by Hiranyamaya Dash. Last updated 3 months ago.
epigeneticsgeneticsqualitycontrolchipseqmultiplecomparisonfunctionalgenomicsmotifdiscoverysequencematchingsoftwarealignmentbioconductorbioconductor-packagechip-seqepigenomicsinteractive-reportmotif-enrichment-analysis
2 stars 5.48 score 6 scriptsbioc
periodicDNA:Set of tools to identify periodic occurrences of k-mers in DNA sequences
This R package helps the user identify k-mers (e.g. di- or tri-nucleotides) present periodically in a set of genomic loci (typically regulatory elements). The functions of this package provide a straightforward approach to find periodic occurrences of k-mers in DNA sequences, such as regulatory elements. It is not aimed at identifying motifs separated by a conserved distance; for this type of analysis, please visit MEME website.
Maintained by Jacques Serizay. Last updated 5 months ago.
sequencematchingmotifdiscoverymotifannotationsequencingcoveragealignmentdataimport
6 stars 5.26 score 5 scriptsbioc
heatmaps:Flexible Heatmaps for Functional Genomics and Sequence Features
This package provides functions for plotting heatmaps of genome-wide data across genomic intervals, such as ChIP-seq signals at peaks or across promoters. Many functions are also provided for investigating sequence features.
Maintained by Malcolm Perry. Last updated 5 months ago.
visualizationsequencematchingfunctionalgenomics
5.23 score 19 scripts 1 dependentsbioc
muscle:Multiple Sequence Alignment with MUSCLE
MUSCLE performs multiple sequence alignments of nucleotide or amino acid sequences.
Maintained by Alex T. Kalinka. Last updated 5 months ago.
multiplesequencealignmentalignmentsequencinggeneticssequencematchingdataimportcpp
5.21 score 81 scriptsbioc
MEDIPS:DNA IP-seq data analysis
MEDIPS was developed for analyzing data derived from methylated DNA immunoprecipitation (MeDIP) experiments followed by sequencing (MeDIP-seq). However, MEDIPS provides functionalities for the analysis of any kind of quantitative sequencing data (e.g. ChIP-seq, MBD-seq, CMS-seq and others) including calculation of differential coverage between groups of samples and saturation and correlation analysis.
Maintained by Lukas Chavez. Last updated 5 months ago.
dnamethylationcpgislanddifferentialexpressionsequencingchipseqpreprocessingqualitycontrolvisualizationmicroarraygeneticscoveragegenomeannotationcopynumbervariationsequencematching
5.17 score 74 scriptsbioc
IMMAN:Interlog protein network reconstruction by Mapping and Mining ANalysis
Reconstructing Interlog Protein Network (IPN) integrated from several Protein protein Interaction Networks (PPINs). Using this package, overlaying different PPINs to mine conserved common networks between diverse species will be applicable.
Maintained by Minoo Ashtiani. Last updated 5 months ago.
sequencematchingalignmentsystemsbiologygraphandnetworknetworkproteomics
5.08 score 3 scriptsbioc
PWMEnrich:PWM enrichment analysis
A toolkit of high-level functions for DNA motif scanning and enrichment analysis built upon Biostrings. The main functionality is PWM enrichment analysis of already known PWMs (e.g. from databases such as MotifDb), but the package also implements high-level functions for PWM scanning and visualisation. The package does not perform "de novo" motif discovery, but is instead focused on using motifs that are either experimentally derived or computationally constructed by other tools.
Maintained by Diego Diez. Last updated 5 months ago.
motifannotationsequencematchingsoftware
5.08 score 60 scriptsbioc
RRHO:Inference on agreement between ordered lists
The package is aimed at inference on the amount of agreement in two sorted lists using the Rank-Rank Hypergeometric Overlap test.
Maintained by Jonathan Rosenblatt. Last updated 5 months ago.
geneticssequencematchingmicroarraytranscription
4.97 score 47 scriptsbioc
motifTestR:Perform key tests for binding motifs in sequence data
Taking a set of sequence motifs as PWMs, test a set of sequences for over-representation of these motifs, as well as any positional features within the set of motifs. Enrichment analysis can be undertaken using multiple statistical approaches. The package also contains core functions to prepare data for analysis, and to visualise results.
Maintained by Stevie Pederson. Last updated 22 days ago.
motifannotationchipseqchiponchipsequencematchingsoftware
1 stars 4.90 score 2 scriptsbioc
BSgenomeForge:Forge your own BSgenome data package
A set of tools to forge BSgenome data packages. Supersedes the old seed-based tools from the BSgenome software package. This package allows the user to create a BSgenome data package in one function call, simplifying the old seed-based process.
Maintained by Hervé Pagès. Last updated 5 months ago.
infrastructuredatarepresentationgenomeassemblyannotationgenomeannotationsequencingalignmentdataimportsequencematchingbioconductor-packagecore-package
4 stars 4.90 score 6 scriptsbioc
rRDP:Interface to the RDP Classifier
This package installs and interfaces the naive Bayesian classifier for 16S rRNA sequences developed by the Ribosomal Database Project (RDP). With this package the classifier trained with the standard training set can be used or a custom classifier can be trained.
Maintained by Michael Hahsler. Last updated 5 months ago.
geneticssequencinginfrastructureclassificationmicrobiomeimmunooncologyalignmentsequencematchingdataimportbayesianbioconductorbioinformaticsopenjdk
3 stars 4.88 score 6 scriptsbioc
packFinder:de novo Annotation of Pack-TYPE Transposable Elements
Algorithm and tools for in silico pack-TYPE transposon discovery. Filters a given genome for properties unique to DNA transposons and provides tools for the investigation of returned matches. Sequences are input in DNAString format, and ranges are returned as a dataframe (in the format returned by as.dataframe(GRanges)).
Maintained by Jack Gisby. Last updated 5 months ago.
geneticssequencematchingannotationbioinformaticstext-mining
7 stars 4.85 score 6 scriptsbioc
seqPattern:Visualising oligonucleotide patterns and motif occurrences across a set of sorted sequences
Visualising oligonucleotide patterns and sequence motifs occurrences across a large set of sequences centred at a common reference point and sorted by a user defined feature.
Maintained by Vanja Haberle. Last updated 5 months ago.
4.78 score 12 scripts 7 dependentsbioc
scanMiRApp:scanMiR shiny application
A shiny interface to the scanMiR package. The application enables the scanning of transcripts and custom sequences for miRNA binding sites, the visualization of KdModels and binding results, as well as browsing predicted repression data. In addition contains the IndexedFst class for fast indexed reading of large GenomicRanges or data.frames, and some utilities for facilitating scans and identifying enriched miRNA-target pairs.
Maintained by Pierre-Luc Germain. Last updated 5 months ago.
mirnasequencematchingguishinyapps
4.76 score 19 scriptsbioc
scoup:Simulate Codons with Darwinian Selection Modelled as an OU Process
An elaborate molecular evolutionary framework that facilitates straightforward simulation of codon genetic sequences subjected to different degrees and/or patterns of Darwinian selection. The model is built upon the fitness landscape paradigm of Sewall Wright, as popularised by the mutation-selection model of Halpern and Bruno. This enables realistic evolutionary process of living organisms to be reproducible seamlessly. For example, an Ornstein-Uhlenbeck fitness update algorithm is incorporated herein. Consequently, otherwise complex biological processes, such as the effect of the interplay between genetic drift and fitness landscape fluctuations on the inference of diversifying selection, may now be investigated with minimal effort. Frequency-dependent and stochastic fitness landscape update techniques are available.
Maintained by Hassan Sadiq. Last updated 3 months ago.
alignmentclassificationcomparativegenomicsdataimportgeneticsmathematicalbiologyresearchfieldsequencingsequencematchingsoftwarestatisticalmethodworkflowstep
4.60 score 8 scriptsbioc
dagLogo:dagLogo: a Bioconductor package for visualizing conserved amino acid sequence pattern in groups based on probability theory
Visualize significant conserved amino acid sequence pattern in groups based on probability theory.
Maintained by Jianhong Ou. Last updated 3 months ago.
4.48 score 9 scriptsbioc
pqsfinder:Identification of potential quadruplex forming sequences
Pqsfinder detects DNA and RNA sequence patterns that are likely to fold into an intramolecular G-quadruplex (G4). Unlike many other approaches, pqsfinder is able to detect G4s folded from imperfect G-runs containing bulges or mismatches or G4s having long loops. Pqsfinder also assigns an integer score to each hit that was fitted on G4 sequencing data and corresponds to expected stability of the folded G4.
Maintained by Jiri Hon. Last updated 5 months ago.
motifdiscoverysequencematchinggeneregulationcpp
4.41 score 16 scriptsbioc
ChIPanalyser:ChIPanalyser: Predicting Transcription Factor Binding Sites
ChIPanalyser is a package to predict and understand TF binding by utilizing a statistical thermodynamic model. The model incorporates 4 main factors thought to drive TF binding: Chromatin State, Binding energy, Number of bound molecules and a scaling factor modulating TF binding affinity. Taken together, ChIPanalyser produces ChIP-like profiles that closely mimic the patterns seens in real ChIP-seq data.
Maintained by Patrick C.N. Martin. Last updated 5 months ago.
softwarebiologicalquestionworkflowsteptranscriptionsequencingchiponchipcoveragealignmentchipseqsequencematchingdataimportpeakdetection
4.38 score 12 scriptsbioc
SynMut:SynMut: Designing Synonymously Mutated Sequences with Different Genomic Signatures
There are increasing demands on designing virus mutants with specific dinucleotide or codon composition. This tool can take both dinucleotide preference and/or codon usage bias into account while designing mutants. It is a powerful tool for in silico designs of DNA sequence mutants.
Maintained by Haogao Gu. Last updated 5 months ago.
sequencematchingexperimentaldesignpreprocessing
2 stars 4.30 score 1 scriptsbioc
motifcounter:R package for analysing TFBSs in DNA sequences
'motifcounter' provides motif matching, motif counting and motif enrichment functionality based on position frequency matrices. The main features of the packages include the utilization of higher-order background models and accounting for self-overlapping motif matches when determining motif enrichment. The background model allows to capture dinucleotide (or higher-order nucleotide) composition adequately which may reduced model biases and misleading results compared to using simple GC background models. When conducting a motif enrichment analysis based on the motif match count, the package relies on a compound Poisson distribution or alternatively a combinatorial model. These distribution account for self-overlapping motif structures as exemplified by repeat-like or palindromic motifs, and allow to determine the p-value and fold-enrichment for a set of observed motif matches.
Maintained by Wolfgang Kopp. Last updated 5 months ago.
transcriptionmotifannotationsequencematchingsoftwareopenmp
4.30 score 7 scriptsbioc
HelloRanges:Introduce *Ranges to bedtools users
Translates bedtools command-line invocations to R code calling functions from the Bioconductor *Ranges infrastructure. This is intended to educate novice Bioconductor users and to compare the syntax and semantics of the two frameworks.
Maintained by Michael Lawrence. Last updated 5 months ago.
sequencingannotationcoveragegenomeannotationdataimportsequencematchingvariantannotation
4.19 score 26 scripts 1 dependentsbioc
XNAString:Efficient Manipulation of Modified Oligonucleotide Sequences
The XNAString package allows for description of base sequences and associated chemical modifications in a single object. XNAString is able to capture single stranded, as well as double stranded molecules. Chemical modifications are represented as independent strings associated with different features of the molecules (base sequence, sugar sequence, backbone sequence, modifications) and can be read or written to a HELM notation. It also enables secondary structure prediction using RNAfold from ViennaRNA. XNAString is designed to be efficient representation of nucleic-acid based therapeutics, therefore it stores information about target sequences and provides interface for matching and alignment functions from Biostrings and pwalign packages.
Maintained by Marianna Plucinska. Last updated 5 months ago.
sequencematchingalignmentsequencinggeneticscpp
4.18 score 4 scriptsbioc
KinSwingR:KinSwingR: network-based kinase activity prediction
KinSwingR integrates phosphosite data derived from mass-spectrometry data and kinase-substrate predictions to predict kinase activity. Several functions allow the user to build PWM models of kinase-subtrates, statistically infer PWM:substrate matches, and integrate these data to infer kinase activity.
Maintained by Ashley J. Waardenberg. Last updated 5 months ago.
proteomicssequencematchingnetwork
4.00 score 4 scriptsbioc
FastqCleaner:A Shiny Application for Quality Control, Filtering and Trimming of FASTQ Files
An interactive web application for quality control, filtering and trimming of FASTQ files. This user-friendly tool combines a pipeline for data processing based on Biostrings and ShortRead infrastructure, with a cutting-edge visual environment. Single-Read and Paired-End files can be locally processed. Diagnostic interactive plots (CG content, per-base sequence quality, etc.) are provided for both the input and output files.
Maintained by Leandro Roser. Last updated 5 months ago.
qualitycontrolsequencingsoftwaresangerseqsequencematchingcpp
4.00 score 4 scriptsbioc
EDIRquery:Query the EDIR Database For Specific Gene
EDIRquery provides a tool to search for genes of interest within the Exome Database of Interspersed Repeats (EDIR). A gene name is a required input, and users can additionally specify repeat sequence lengths, minimum and maximum distance between sequences, and whether to allow a 1-bp mismatch. Outputs include a summary of results by repeat length, as well as a dataframe of query results. Example data provided includes a subset of the data for the gene GAA (ENSG00000171298). To query the full database requires providing a path to the downloaded database files as a parameter.
Maintained by Laura D.T. Vo Ngoc. Last updated 5 months ago.
4.00 score 1 scriptsbioc
Motif2Site:Detect binding sites from motifs and ChIP-seq experiments, and compare binding sites across conditions
Detect binding sites using motifs IUPAC sequence or bed coordinates and ChIP-seq experiments in bed or bam format. Combine/compare binding sites across experiments, tissues, or conditions. All normalization and differential steps are done using TMM-GLM method. Signal decomposition is done by setting motifs as the centers of the mixture of normal distribution curves.
Maintained by Peyman Zarrineh. Last updated 5 months ago.
softwaresequencingchipseqdifferentialpeakcallingepigeneticssequencematching
4.00 score 3 scriptsbioc
bcSeq:Fast Sequence Mapping in High-Throughput shRNA and CRISPR Screens
This Rcpp-based package implements a highly efficient data structure and algorithm for performing alignment of short reads from CRISPR or shRNA screens to reference barcode library. Sequencing error are considered and matching qualities are evaluated based on Phred scores. A Bayes' classifier is employed to predict the originating barcode of a read. The package supports provision of user-defined probability models for evaluating matching qualities. The package also supports multi-threading.
Maintained by Jiaxing Lin. Last updated 5 months ago.
immunooncologyalignmentcrisprsequencingsequencematchingmultiplesequencealignmentsoftwareatacseqcpp
3.78 score 2 scriptsbioc
REDseq:Analysis of high-throughput sequencing data processed by restriction enzyme digestion
The package includes functions to build restriction enzyme cut site (RECS) map, distribute mapped sequences on the map with five different approaches, find enriched/depleted RECSs for a sample, and identify differentially enriched/depleted RECSs between samples.
Maintained by Lihua Julie Zhu. Last updated 5 months ago.
sequencingsequencematchingpreprocessing
3.48 score 15 scriptsbioc
DominoEffect:Identification and Annotation of Protein Hotspot Residues
The functions support identification and annotation of hotspot residues in proteins. These are individual amino acids that accumulate mutations at a much higher rate than their surrounding regions.
Maintained by Marija Buljan. Last updated 5 months ago.
softwaresomaticmutationproteomicssequencematchingalignment
3.48 score 1 scriptsbioc
MethTargetedNGS:Perform Methylation Analysis on Next Generation Sequencing Data
Perform step by step methylation analysis of Next Generation Sequencing data.
Maintained by Muhammad Ahmer Jamil. Last updated 5 months ago.
researchfieldgeneticssequencingalignmentsequencematchingdataimport
3.48 score 1 scriptsbioc
microRNA:Data and functions for dealing with microRNAs
Different data resources for microRNAs and some functions for manipulating them.
Maintained by "Michael Lawrence". Last updated 2 months ago.
infrastructuregenomeannotationsequencematchingcpp
3.48 score 7 scriptsbioc
SimFFPE:NGS Read Simulator for FFPE Tissue
The NGS (Next-Generation Sequencing) reads from FFPE (Formalin-Fixed Paraffin-Embedded) samples contain numerous artifact chimeric reads (ACRS), which can lead to false positive structural variant calls. These ACRs are derived from the combination of two single-stranded DNA (ss-DNA) fragments with short reverse complementary regions (SRCRs). This package simulates these artifact chimeric reads as well as normal reads for FFPE samples on the whole genome / several chromosomes / large regions.
Maintained by Lanying Wei. Last updated 5 months ago.
sequencingalignmentmultiplecomparisonsequencematchingdataimport
3.30 score 1 scriptsbioc
SICtools:Find SNV/Indel differences between two bam files with near relationship
This package is to find SNV/Indel differences between two bam files with near relationship in a way of pairwise comparison thourgh each base position across the genome region of interest. The difference is inferred by fisher test and euclidean distance, the input of which is the base count (A,T,G,C) in a given position and read counts for indels that span no less than 2bp on both sides of indel region.
Maintained by Xiaobin Xing. Last updated 5 months ago.
alignmentsequencingcoveragesequencematchingqualitycontroldataimportsoftwaresnpvariantdetection
3.30 score 1 scriptsbioc
hapFabia:hapFabia: Identification of very short segments of identity by descent (IBD) characterized by rare variants in large sequencing data
A package to identify very short IBD segments in large sequencing data by FABIA biclustering. Two haplotypes are identical by descent (IBD) if they share a segment that both inherited from a common ancestor. Current IBD methods reliably detect long IBD segments because many minor alleles in the segment are concordant between the two haplotypes. However, many cohort studies contain unrelated individuals which share only short IBD segments. This package provides software to identify short IBD segments in sequencing data. Knowledge of short IBD segments are relevant for phasing of genotyping data, association studies, and for population genetics, where they shed light on the evolutionary history of humans. The package supports VCF formats, is based on sparse matrix operations, and provides visualization of haplotype clusters in different formats.
Maintained by Andreas Mitterecker. Last updated 5 months ago.
geneticsgeneticvariabilitysnpsequencingvisualizationclusteringsequencematchingsoftware
3.30 score 9 scriptsbioc
Basic4Cseq:Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data
Basic4Cseq is an R/Bioconductor package for basic filtering, analysis and subsequent visualization of 4C-seq data. Virtual fragment libraries can be created for any BSGenome package, and filter functions for both reads and fragments and basic quality controls are included. Fragment data in the vicinity of the experiment's viewpoint can be visualized as a coverage plot based on a running median approach and a multi-scale contact profile.
Maintained by Carolin Walter. Last updated 5 months ago.
immunooncologyvisualizationqualitycontrolsequencingcoveragealignmentrnaseqsequencematchingdataimport
3.30 score 5 scriptsbioc
ipdDb:IPD IMGT/HLA and IPD KIR database for Homo sapiens
All alleles from the IPD IMGT/HLA <https://www.ebi.ac.uk/ipd/imgt/hla/> and IPD KIR <https://www.ebi.ac.uk/ipd/kir/> database for Homo sapiens. Reference: Robinson J, Maccari G, Marsh SGE, Walter L, Blokhuis J, Bimber B, Parham P, De Groot NG, Bontrop RE, Guethlein LA, and Hammond JA KIR Nomenclature in non-human species Immunogenetics (2018), in preparation.
Maintained by Steffen Klasberg. Last updated 5 months ago.
genomicvariationsequencematchingvariantannotationdatarepresentationannotationhubsoftware
3.30 score 4 scriptsbioc
triplex:Search and visualize intramolecular triplex-forming sequences in DNA
This package provides functions for identification and visualization of potential intramolecular triplex patterns in DNA sequence. The main functionality is to detect the positions of subsequences capable of folding into an intramolecular triplex (H-DNA) in a much larger sequence. The potential H-DNA (triplexes) should be made of as many cannonical nucleotide triplets as possible. The package includes visualization showing the exact base-pairing in 1D, 2D or 3D.
Maintained by Jiri Hon. Last updated 5 months ago.
sequencematchinggeneregulation
3.30 score 2 scripts