bioconductor.org "Alignment" keyword
Top 1.7% on bioconductor.org
12 versions - Latest release: about 2 months ago - 28 dependent packages - 2.26 million downloads total - 1 maintainer
ggtree 4.0.4
an R package for visualization of tree and annotation data12 versions - Latest release: about 2 months ago - 28 dependent packages - 2.26 million downloads total - 1 maintainer
Top 1.8% on bioconductor.org
8 versions - Latest release: 4 months ago - 14 dependent packages - 417 thousand downloads total - 2 maintainers
Rsubread 2.24.0
Mapping, quantification and variant analysis of sequencing data8 versions - Latest release: 4 months ago - 14 dependent packages - 417 thousand downloads total - 2 maintainers
Top 0.6% on bioconductor.org
8 versions - Latest release: 4 months ago - 132 dependent packages - 4.92 million downloads total - 1 maintainer
GenomicAlignments 1.46.0
Representation and manipulation of short genomic alignments8 versions - Latest release: 4 months ago - 132 dependent packages - 4.92 million downloads total - 1 maintainer
Top 0.2% on bioconductor.org
11 versions - Latest release: 4 months ago - 333 dependent packages - 9.37 million downloads total - 1 maintainer
Biostrings 2.78.0
Efficient manipulation of biological strings11 versions - Latest release: 4 months ago - 333 dependent packages - 9.37 million downloads total - 1 maintainer
VplotR 1.20.0
Set of tools to make V-plots and compute footprint profiles7 versions - Latest release: 3 months ago - 10.6 thousand downloads total - 11 stars on GitHub - 1 maintainer
scruff 1.28.0
Single Cell RNA-Seq UMI Filtering Facilitator (scruff)7 versions - Latest release: 3 months ago - 14.6 thousand downloads total - 8 stars on GitHub - 1 maintainer
XNAString 1.18.0
Efficient Manipulation of Modified Oligonucleotide Sequences6 versions - Latest release: 4 months ago - 7.72 thousand downloads total - 1 maintainer
txcutr 1.16.0
Transcriptome CUTteR6 versions - Latest release: 4 months ago - 7.89 thousand downloads total - 1 maintainer
normr 1.36.0
Normalization and difference calling in ChIP-seq data6 versions - Latest release: 3 months ago - 24.4 thousand downloads total - 11 stars on GitHub - 1 maintainer
rBLAST 1.6.0
R Interface for the Basic Local Alignment Search Tool4 versions - Latest release: 4 months ago - 8.53 thousand downloads total - 112 stars on GitHub - 1 maintainer
cigarillo 1.0.0
Efficient manipulation of CIGAR strings1 version - Latest release: 4 months ago - 84.5 thousand downloads total - 1 maintainer
RbowtieCuda 1.2.0
An R Wrapper for nvBowtie and nvBWT, a rewritten version of Bowtie2 for cuda5 versions - Latest release: 3 months ago - 2.08 thousand downloads total - 2 stars on GitHub - 1 maintainer
ompBAM 1.14.0
C++ Library for OpenMP-based multi-threaded sequential profiling of Binary Alignment Map (BAM) files6 versions - Latest release: 3 months ago - 1 dependent package - 9.48 thousand downloads total - 4 stars on GitHub - 1 maintainer
surfaltr 1.16.0
Rapid Comparison of Surface Protein Isoform Membrane Topologies Through surfaltr6 versions - Latest release: 4 months ago - 8.55 thousand downloads total - 1 maintainer
ggseqalign 1.4.0
Minimal Visualization of Sequence Alignments3 versions - Latest release: 3 months ago - 3.46 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 0.4% on bioconductor.org
4 versions - Latest release: over 1 year ago - 212 dependent packages - 4.22 million downloads total - 1 maintainer
Rsamtools 2.22.0
Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import4 versions - Latest release: over 1 year ago - 212 dependent packages - 4.22 million downloads total - 1 maintainer
strandCheckR 1.28.0
Calculate strandness information of a bam file6 versions - Latest release: 4 months ago - 12.6 thousand downloads total - 0 stars on GitHub - 1 maintainer
mitoClone2 1.16.0
Clonal Population Identification in Single-Cell RNA-Seq Data using Mitochondrial and Somatic Muta...7 versions - Latest release: 3 months ago - 8.45 thousand downloads total - 1 stars on GitHub - 1 maintainer
recoup 1.38.0
An R package for the creation of complex genomic profile plots6 versions - Latest release: 3 months ago - 19.2 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 6.7% on bioconductor.org
6 versions - Latest release: 3 months ago - 44.9 thousand downloads total - 0 stars on GitHub - 1 maintainer
segmentSeq 2.44.0
Methods for identifying small RNA loci from high-throughput sequencing data6 versions - Latest release: 3 months ago - 44.9 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 3.1% on bioconductor.org
6 versions - Latest release: 3 months ago - 7 dependent packages - 1.91 million downloads total - 1 maintainer
treeio 1.34.0
Base Classes and Functions for Phylogenetic Tree Input and Output6 versions - Latest release: 3 months ago - 7 dependent packages - 1.91 million downloads total - 1 maintainer
scoup 1.4.0
Simulate Codons with Darwinian Selection Modelled as an OU Process3 versions - Latest release: 3 months ago - 3.19 thousand downloads total - 0 stars on GitHub - 1 maintainer
CircSeqAlignTk 1.12.0
End-to-End Analysis of Small RNA-Seq Data from Viroids6 versions - Latest release: 4 months ago - 6.47 thousand downloads total - 0 stars on GitHub - 1 maintainer
enhancerHomologSearch 1.16.0
Identification of putative mammalian orthologs to given enhancer8 versions - Latest release: 3 months ago - 8.28 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 4.5% on bioconductor.org
6 versions - Latest release: 3 months ago - 17 dependent packages - 478 thousand downloads total - 30 stars on GitHub - 1 maintainer
TFBSTools 1.48.0
Software Package for Transcription Factor Binding Site (TFBS) Analysis6 versions - Latest release: 3 months ago - 17 dependent packages - 478 thousand downloads total - 30 stars on GitHub - 1 maintainer
esATAC 1.32.0
An Easy-to-use Systematic pipeline for ATACseq data analysis6 versions - Latest release: 3 months ago - 27 thousand downloads total - 23 stars on GitHub - 1 maintainer
rprimer 1.14.0
Design Degenerate Oligos from a Multiple DNA Sequence Alignment6 versions - Latest release: 3 months ago - 8.51 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 3.4% on bioconductor.org
7 versions - Latest release: 3 months ago - 2 dependent packages - 114 thousand downloads total - 1 maintainer
QuasR 1.50.0
Quantify and Annotate Short Reads in R7 versions - Latest release: 3 months ago - 2 dependent packages - 114 thousand downloads total - 1 maintainer
nucleoSim 1.38.0
Generate synthetic nucleosome maps6 versions - Latest release: 3 months ago - 1 dependent package - 17.1 thousand downloads total - 2 stars on GitHub - 1 maintainer
crisprBowtie 1.14.0
Bowtie-based alignment of CRISPR gRNA spacer sequences6 versions - Latest release: 3 months ago - 2 dependent packages - 13.1 thousand downloads total - 3 stars on GitHub - 1 maintainer
periodicDNA 1.20.0
Set of tools to identify periodic occurrences of k-mers in DNA sequences6 versions - Latest release: 3 months ago - 10.1 thousand downloads total - 6 stars on GitHub - 1 maintainer
UMI4Cats 1.20.0
UMI4Cats: Processing, analysis and visualization of UMI-4C chromatin contact data8 versions - Latest release: 3 months ago - 10.2 thousand downloads total - 5 stars on GitHub - 1 maintainer
amplican 1.32.1
Automated analysis of CRISPR experiments6 versions - Latest release: 3 months ago - 22.1 thousand downloads total - 9 stars on GitHub - 1 maintainer
Rhisat2 1.26.0
R Wrapper for HISAT2 Aligner6 versions - Latest release: 3 months ago - 3 dependent packages - 32.3 thousand downloads total - 3 stars on GitHub - 1 maintainer
IntEREst 1.34.0
Intron-Exon Retention Estimator8 versions - Latest release: 3 months ago - 18.4 thousand downloads total - 1 maintainer
screenCounter 1.10.0
Counting Reads in High-Throughput Sequencing Screens6 versions - Latest release: 3 months ago - 6.37 thousand downloads total - 3 stars on GitHub - 1 maintainer
LinTInd 1.14.0
Lineage tracing by indels6 versions - Latest release: 3 months ago - 7.73 thousand downloads total - 1 maintainer
BSgenomeForge 1.10.2
Forge your own BSgenome data package11 versions - Latest release: 2 months ago - 1 dependent package - 17.3 thousand downloads total - 1 maintainer
KnowSeq 1.24.0
KnowSeq R/Bioc package: The Smart Transcriptomic Pipeline6 versions - Latest release: 3 months ago - 13.8 thousand downloads total - 1 maintainer
Guitar 2.26.0
Guitar6 versions - Latest release: 3 months ago - 30.9 thousand downloads total - 1 maintainer
TVTB 1.36.0
TVTB: The VCF Tool Box8 versions - Latest release: 4 months ago - 16.6 thousand downloads total - 2 stars on GitHub - 1 maintainer
ORFik 1.30.2
Open Reading Frames in Genomics13 versions - Latest release: 2 months ago - 2 dependent packages - 32.3 thousand downloads total - 34 stars on GitHub - 1 maintainer
pwalign 1.6.0
Perform pairwise sequence alignments4 versions - Latest release: 3 months ago - 9 dependent packages - 239 thousand downloads total - 1 maintainer
SICtools 1.40.0
Find SNV/Indel differences between two bam files with near relationship6 versions - Latest release: 3 months ago - 17.6 thousand downloads total - 1 maintainer
traseR 1.40.0
GWAS trait-associated SNP enrichment analyses in genomic intervals6 versions - Latest release: 3 months ago - 18.9 thousand downloads total
diffHic 1.42.0
Differential Analysis of Hi-C Data6 versions - Latest release: 3 months ago - 33.3 thousand downloads total - 3 maintainers
FilterFFPE 1.20.0
FFPE Artificial Chimeric Read Filter for NGS data6 versions - Latest release: 3 months ago - 9.54 thousand downloads total - 1 maintainer
sangeranalyseR 1.20.0
sangeranalyseR: a suite of functions for the analysis of Sanger sequence data in R6 versions - Latest release: 3 months ago - 21.7 thousand downloads total - 1 maintainer
mobileRNA 1.6.1
mobileRNA: Investigate the RNA mobilome & population-scale changes9 versions - Latest release: 26 days ago - 4.93 thousand downloads total - 1 maintainer
raer 1.8.0
RNA editing tools in R6 versions - Latest release: 3 months ago - 5.82 thousand downloads total - 10 stars on GitHub - 1 maintainer
Rbwa 1.14.0
R wrapper for BWA-backtrack and BWA-MEM aligners6 versions - Latest release: 3 months ago - 2 dependent packages - 8.52 thousand downloads total - 1 maintainer
Top 2.8% on bioconductor.org
6 versions - Latest release: 3 months ago - 7 dependent packages - 352 thousand downloads total - 1 maintainer
DECIPHER 3.6.0
Tools for curating, analyzing, and manipulating biological sequences6 versions - Latest release: 3 months ago - 7 dependent packages - 352 thousand downloads total - 1 maintainer
seqcombo 1.32.0
Visualization Tool for Genetic Reassortment6 versions - Latest release: 3 months ago - 14.7 thousand downloads total - 21 stars on GitHub - 1 maintainer
Top 5.9% on bioconductor.org
6 versions - Latest release: 4 months ago - 60.6 thousand downloads total - 1 maintainer
muscle 3.52.0
Multiple Sequence Alignment with MUSCLE6 versions - Latest release: 4 months ago - 60.6 thousand downloads total - 1 maintainer
Basic4Cseq 1.46.0
Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data6 versions - Latest release: 3 months ago - 29.9 thousand downloads total - 1 maintainer
ncGTW 1.24.0
Alignment of LC-MS Profiles by Neighbor-wise Compound-specific Graphical Time Warping with Misali...6 versions - Latest release: 3 months ago - 11.3 thousand downloads total - 1 maintainer
DominoEffect 1.30.0
Identification and Annotation of Protein Hotspot Residues6 versions - Latest release: 3 months ago - 13.6 thousand downloads total - 2 maintainers
RcwlPipelines 1.26.0
Bioinformatics pipelines based on Rcwl7 versions - Latest release: 3 months ago - 1 dependent package - 13.6 thousand downloads total - 1 maintainer
RiboProfiling 1.39.1
Ribosome Profiling Data Analysis: from BAM to Data Representation and Interpretation6 versions - Latest release: 3 months ago - 25.3 thousand downloads total - 1 maintainer
singleCellTK 2.20.1
Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data11 versions - Latest release: 26 days ago - 1 dependent package - 38.4 thousand downloads total - 1 maintainer
ChIPexoQual 1.34.0
ChIPexoQual6 versions - Latest release: 3 months ago - 19.1 thousand downloads total - 1 stars on GitHub - 1 maintainer
tanggle 1.16.0
Visualization of Phylogenetic Networks6 versions - Latest release: 3 months ago - 8.75 thousand downloads total - 10 stars on GitHub - 1 maintainer
assorthead 1.4.0
Assorted Header-Only C++ Libraries4 versions - Latest release: 3 months ago - 308 thousand downloads total - 1 stars on GitHub - 1 maintainer
transmogR 1.6.0
Modify a set of reference sequences using a set of variants7 versions - Latest release: 3 months ago - 4.79 thousand downloads total - 0 stars on GitHub - 1 maintainer
QSutils 1.28.0
Quasispecies Diversity6 versions - Latest release: 3 months ago - 27.6 thousand downloads total - 1 maintainer
MotifPeeker 1.2.0
Benchmarking Epigenomic Profiling Methods Using Motif Enrichment2 versions - Latest release: 3 months ago - 2.74 thousand downloads total - 2 stars on GitHub - 1 maintainer
ChIPanalyser 1.32.0
ChIPanalyser: Predicting Transcription Factor Binding Sites6 versions - Latest release: 3 months ago - 15.7 thousand downloads total - 1 maintainer
ASpli 2.20.0
Analysis of Alternative Splicing Using RNA-Seq6 versions - Latest release: 3 months ago - 1 dependent package - 28.8 thousand downloads total - 1 maintainer
gmapR 1.51.1
An R interface to the GMAP/GSNAP/GSTRUCT suite6 versions - Latest release: 3 months ago - 3 dependent packages - 37.1 thousand downloads total - 1 maintainer
gDNAx 1.8.2
Diagnostics for assessing genomic DNA contamination in RNA-seq data11 versions - Latest release: 2 months ago - 6.32 thousand downloads total - 1 stars on GitHub - 1 maintainer
SCOPE 1.22.0
A normalization and copy number estimation method for single-cell DNA sequencing6 versions - Latest release: 3 months ago - 11.3 thousand downloads total - 1 maintainer
LymphoSeq 1.38.0
Analyze high-throughput sequencing of T and B cell receptors6 versions - Latest release: 3 months ago - 19.1 thousand downloads total - 1 maintainer
R4RNA 1.38.0
An R package for RNA visualization and analysis6 versions - Latest release: 3 months ago - 2 dependent packages - 56.6 thousand downloads total - 1 maintainer
SimFFPE 1.22.0
NGS Read Simulator for FFPE Tissue6 versions - Latest release: 3 months ago - 9.3 thousand downloads total - 1 maintainer
RiboDiPA 1.18.0
Differential pattern analysis for Ribo-seq data6 versions - Latest release: 3 months ago - 9.31 thousand downloads total - 1 maintainer
DegNorm 1.20.0
DegNorm: degradation normalization for RNA-seq data6 versions - Latest release: 3 months ago - 10.7 thousand downloads total - 1 stars on GitHub - 1 maintainer
Structstrings 1.26.0
Implementation of the dot bracket annotations with Biostrings7 versions - Latest release: 3 months ago - 3 dependent packages - 16.9 thousand downloads total - 5 stars on GitHub - 1 maintainer
Top 5.9% on bioconductor.org
8 versions - Latest release: 26 days ago - 3 dependent packages - 276 thousand downloads total - 54 stars on GitHub - 1 maintainer
systemPipeR 2.16.3
systemPipeR: Workflow Environment for Data Analysis and Report Generation8 versions - Latest release: 26 days ago - 3 dependent packages - 276 thousand downloads total - 54 stars on GitHub - 1 maintainer
MethTargetedNGS 1.42.0
Perform Methylation Analysis on Next Generation Sequencing Data6 versions - Latest release: 3 months ago - 18.1 thousand downloads total - 1 maintainer
ggmsa 1.16.0
Plot Multiple Sequence Alignment using 'ggplot2'7 versions - Latest release: 3 months ago - 45.8 thousand downloads total - 1 maintainer
Top 2.8% on bioconductor.org
7 versions - Latest release: 3 months ago - 4 dependent packages - 278 thousand downloads total - 21 stars on GitHub - 1 maintainer
msa 1.42.0
Multiple Sequence Alignment7 versions - Latest release: 3 months ago - 4 dependent packages - 278 thousand downloads total - 21 stars on GitHub - 1 maintainer
bcSeq 1.32.0
Fast Sequence Mapping in High-Throughput shRNA and CRISPR Screens6 versions - Latest release: 3 months ago - 14.5 thousand downloads total - 0 stars on GitHub - 1 maintainer
ptairMS 1.18.0
Pre-processing PTR-TOF-MS Data6 versions - Latest release: 3 months ago - 9.24 thousand downloads total - 7 stars on GitHub - 1 maintainer
Rbowtie2 2.16.0
An R Wrapper for Bowtie2 and AdapterRemoval7 versions - Latest release: 3 months ago - 3 dependent packages - 45.1 thousand downloads total - 1 maintainer
Top 3.6% on bioconductor.org
6 versions - Latest release: 3 months ago - 10 dependent packages - 150 thousand downloads total - 1 maintainer
motifStack 1.54.0
Plot stacked logos for single or multiple DNA, RNA and amino acid sequence6 versions - Latest release: 3 months ago - 10 dependent packages - 150 thousand downloads total - 1 maintainer
metagene2 1.26.0
A package to produce metagene plots6 versions - Latest release: 3 months ago - 13.8 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 5.7% on bioconductor.org
6 versions - Latest release: 3 months ago - 2 dependent packages - 127 thousand downloads total - 1 maintainer
GreyListChIP 1.42.0
Grey Lists -- Mask Artefact Regions Based on ChIP Inputs6 versions - Latest release: 3 months ago - 2 dependent packages - 127 thousand downloads total - 1 maintainer
scanMiR 1.16.0
scanMiR7 versions - Latest release: 3 months ago - 1 dependent package - 9.47 thousand downloads total - 1 maintainer
Top 4.6% on bioconductor.org
6 versions - Latest release: 3 months ago - 7 dependent packages - 155 thousand downloads total - 15 stars on GitHub - 1 maintainer
bamsignals 1.42.0
Extract read count signals from bam files6 versions - Latest release: 3 months ago - 7 dependent packages - 155 thousand downloads total - 15 stars on GitHub - 1 maintainer
BadRegionFinder 1.38.0
BadRegionFinder: an R/Bioconductor package for identifying regions with bad coverage6 versions - Latest release: 3 months ago - 19.3 thousand downloads total - 1 maintainer
BBCAnalyzer 1.40.0
BBCAnalyzer: an R/Bioconductor package for visualizing base counts6 versions - Latest release: 3 months ago - 21.4 thousand downloads total - 1 maintainer
chimeraviz 1.36.0
Visualization tools for gene fusions6 versions - Latest release: 3 months ago - 24.3 thousand downloads total - 38 stars on GitHub - 1 maintainer
odseq 1.38.0
Outlier detection in multiple sequence alignments6 versions - Latest release: 3 months ago - 17.1 thousand downloads total - 1 maintainer
OUTRIDER 1.28.0
OUTRIDER - OUTlier in RNA-Seq fInDER9 versions - Latest release: 3 months ago - 1 dependent package - 28 thousand downloads total - 53 stars on GitHub - 1 maintainer
IMMAN 1.30.0
Interlog protein network reconstruction by Mapping and Mining ANalysis6 versions - Latest release: 3 months ago - 13.6 thousand downloads total - 1 maintainer
DiffLogo 2.34.0
DiffLogo: A comparative visualisation of biooligomer motifs6 versions - Latest release: 3 months ago - 20.1 thousand downloads total - 8 stars on GitHub
rRDP 1.44.0
Interface to the RDP Classifier6 versions - Latest release: 3 months ago - 21.2 thousand downloads total - 3 stars on GitHub - 1 maintainer
crisprBwa 1.14.0
BWA-based alignment of CRISPR gRNA spacer sequences6 versions - Latest release: 3 months ago - 1 dependent package - 8.22 thousand downloads total - 1 stars on GitHub - 1 maintainer
MSA2dist 1.14.0
MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet u...6 versions - Latest release: 3 months ago - 1 dependent package - 10.7 thousand downloads total - 1 maintainer
Top 4.2% on bioconductor.org
6 versions - Latest release: 3 months ago - 5 dependent packages - 90.7 thousand downloads total - 1 stars on GitHub - 1 maintainer
Rbowtie 1.50.0
R bowtie wrapper6 versions - Latest release: 3 months ago - 5 dependent packages - 90.7 thousand downloads total - 1 stars on GitHub - 1 maintainer
Related Keywords
Software
107
Sequencing
73
DataImport
42
Coverage
36
QualityControl
29
SequenceMatching
28
Genetics
26
RNASeq
23
ImmunoOncology
23
Preprocessing
19
Visualization
18
MultipleSequenceAlignment
16
MultipleComparison
14
ChIPSeq
12
GeneExpression
11
Normalization
11
DifferentialExpression
10
bioconductor
9
SingleCell
9
Infrastructure
8
DataRepresentation
8
Annotation
8
SNP
7
Transcription
7
FunctionalGenomics
7
Clustering
7
CRISPR
6
Transcriptomics
6
WorkflowStep
6
r
5
DNASeq
5
Classification
5
WholeGenome
5
GenomeAnnotation
5
SplicedAlignment
4
GeneticVariability
4
GeneRegulation
4
MotifAnnotation
4
ATACSeq
4
RiboSeq
4
bioconductor-package
4
bioinformatics
4
Phylogenetics
4
MotifDiscovery
3
qPCR
3
GenomeAssembly
3
MethylSeq
3
BatchEffect
3
FeatureExtraction
3
Microarray
3
Technology
3
GUI
3
PeakDetection
3
VariantAnnotation
3
Proteomics
3
Metabolomics
3
MassSpectrometry
3
grna-sequence
2
grna
2
crispr-target
2
rna-seq-analysis
2
crispr-design
2
crispr-cas9
2
crispr-analysis
2
crispr
2
Microbiome
2
VariantDetection
2
grna-sequences
2
rna-seq
2
TargetedResequencing
2
GenomicVariation
2
sgrna
2
sgrna-design
2
AlternativeSplicing
2
DifferentialSplicing
2
SomaticMutation
2
GO
2
GeneSetEnrichment
2
SystemsBiology
2
BiologicalQuestion
2
Bayesian
2
DifferentialPeakCalling
2
ChipOnChip
2
ResearchField
2
StatisticalMethod
2
SmallRNA
2
aligner
2
count-data
1
miRNA
1
ChIPchip
1
WorkflowManagement
1
ReportWriting
1
structures
1
sequences
1
rna-structure
1
rna-structural-analysis
1
rna
1
GeneFusionDetection
1
CopyNumberVariation
1
TimeCourse
1