seqinr: Biological Sequences Retrieval and Analysis

Canonical link: https://rscholar.com/pkg/seqinr

Delphine Charif • Olivier Clerc • Carolin Frank • Jean R. Lobry • Anamaria Necşulea • Leonor Palmeira • Simon Penel • Guy Perrière • View description and downloads View dependencies GitHub project

2014 Published

4.2-36 Version

0 Citations

8 Authors

Referenced by ⇅	Year
BALCONY: Better ALignment CONsensus analYsis (Version 0.2.10)	2017
caRpools: CRISPR AnalyzeR for Pooled CRISPR Screens (Version 0.83)	2015
ggcoverage: Visualize Genome Coverage with Various Annotations (Version 0.7.1)	2022
SimRAD: Simulations to Predict the Number of RAD and GBS Loci (Version 0.96)	2014
comradesOO: Analysis of COMRADES (Cross-Linking Matched RNA and Deep Sequencing) Data (Version 0.1.1)	2023
metacoder: Tools for Parsing, Manipulating, and Graphing Taxonomic Abundance Data (Version 0.3.7)	2016
effectR: Predicts Oomycete Effectors (Version 1.0.2)	2018
AmyloGram: Prediction of Amyloid Proteins (Version 1.1)	2016
AnnotationBustR: Extract Subsequences from GenBank Annotations (Version 1.3.0)	2017
Autoplotprotein: Development of Visualization Tools for Protein Sequence (Version 1.1)	2017
CovidMutations: Mutation Analysis Toolkit for COVID-19 (Coronavirus Disease 2019) (Version 0.1.3)	2020
DCODE: List Linear n-Peptide Constraints for Overlapping Protein Regions (Version 1.0)	2016
EnsCat: Clustering of Categorical Data (Version 1.1)	2017
EnvNJ: Whole Genome Phylogenies Using Sequence Environments (Version 0.1.3)	2021
EpiSemble: Ensemble Based Machine Learning Approach for Predicting Methylation States (Version 0.1.1)	2022
GB5mcPred: Gradient Boosting Algorithm for Predicting Methylation States (Version 0.1.0)	2023
GenomicSig: Computation of Genomic Signatures (Version 0.1.0)	2024
HextractoR: Integrated Tool for Hairping Extraction of RNA Sequences (Version 1.4)	2018
LSPFP: Lysate and Secretome Peptide Feature Plotter (Version 1.0.3)	2016
LncFinder: LncRNA Identification and Analysis Using Heterologous Features (Version 1.1.6)	2017
MAGNAMWAR: A Pipeline for Meta-Genome Wide Association (Version 2.0.4)	2017
MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis (Version 0.10.1)	2024
OpEnHiMR: Optimization Based Ensemble Model for Prediction of Histone Modifications in Rice (Version 0.1.1)	2024
PTXQC: Quality Report Generation for MaxQuant and mzTab Results (Version 1.1.1)	2016
Platypus: Single-Cell Immune Repertoire and Gene Expression Analysis (Version 3.6.0)	2021
RHybridFinder: Identification of Hybrid Peptides in Immunopeptidomic Analyses (Version 0.2.0)	2021
RScelestial: Scelestial: Steiner Tree Based Single-Cell Lineage Tree Inference (Version 1.0.4)	2019
SMM: Simulation and Estimation of Multi-State Discrete-Time Semi-Markov and Markov Models (Version 1.0.2)	2017
aLFQ: Estimating Absolute Protein Quantities from Label-Free LC-MS/MS Proteomics Data (Version 1.3.6)	2013
adegenet: Exploratory Analysis of Genetic and Genomic Data (Version 2.1.10)	2007
agvgd: An R Implementation of the 'Align-GVGD' Method (Version 0.1.2)	2022
alakazam: Immunoglobulin Clonal Lineage and Diversity Analysis (Version 1.3.0)	2016
beautier: 'BEAUti' from R (Version 2.6.12)	2018
biomartr: Genomic Data Retrieval (Version 1.0.7)	2015
coil: Contextualization and Evaluation of COI-5P Barcode Data (Version 1.2.4)	2019
copyseparator: Assembling Long Gene Copies from Short Read Data (Version 1.2.0)	2022
cubfits: Codon Usage Bias Fits (Version 0.1-4)	2014
dartR.base: Analysing 'SNP' and 'Silicodart' Data - Basic Functions (Version 0.98)	2023
dartR: Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis (Version 2.9.7)	2017
debar: A Post-Clustering Denoiser for COI-5P Barcode Data (Version 0.1.1)	2019
deepredeff: Deep Learning Prediction of Effectors (Version 0.1.1)	2020
disprose: Discriminating Probes Selection (Version 0.1.6)	2021
drimmR: Estimation, Simulation and Reliability of Drifting Markov Models (Version 1.0.1)	2021
evobiR: Comparative and Population Genetic Analyses (Version 1.1)	2013
file2meco: Transform Files to 'microtable' Object with 'microeco' Package (Version 0.8.0)	2021
gkmSVM: Gapped-Kmer Support Vector Machine (Version 0.83.0)	2015
gquad: Prediction of G Quadruplexes and Other Non-B DNA Motifs (Version 2.1-2)	2015
hoardeR: Collect and Retrieve Annotation Data for Various Genomic Data Using Different Webservices (Version 0.10)	2014
insect: Informatic Sequence Classification Trees (Version 1.4.2)	2018
itol.toolkit: Helper Functions for 'Interactive Tree Of Life' (Version 1.1.7)	2023
longreadvqs: Viral Quasispecies Comparison from Long-Read Sequencing Data (Version 0.1.3)	2024
metaCluster: Metagenomic Clustering (Version 0.1.1)	2021
netmhc2pan: Interface to 'NetMHCIIpan' (Version 1.3.2)	2020
orthGS: Orthology vs Paralogy Relationships among Glutamine Synthetase from Plants (Version 0.1.5)	2024
phangorn: Phylogenetic Reconstruction and Analysis (Version 2.12.1)	2008
plotprotein: Development of Visualization Tools for Protein Sequence (Version 1.0)	2017
prozor: Minimal Protein Set Explaining Peptide Spectrum Matches (Version 0.3.1)	2015
rnaCrosslinkOO: Analysis of RNA Crosslinking Data (Version 0.1.4)	2024
seq2R: Simple Method to Detect Compositional Changes in Genomic Sequences (Version 2.0.1)	2012
shazam: Immunoglobulin Somatic Hypermutation Analysis (Version 1.2.0)	2016
signalHsmm: Predict Presence of Signal Peptides (Version 1.5)	2015
smmR: Simulation, Estimation and Reliability of Semi-Markov Models (Version 1.0.3)	2021
spgs: Statistical Patterns in Genomic Sequences (Version 1.0-4)	2017
tidysq: Tidy Processing and Analysis of Biological Sequences (Version 1.2.2)	2021
vhcub: Virus-Host Codon Usage Co-Adaptation Analysis (Version 1.0.0)	2019
vhica: Vertical and Horizontal Inheritance Consistence Analysis (Version 0.2.8)	2016
vivaldi: Viral Variant Location and Diversity (Version 1.0.1)	2022

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