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146 search results found
Adam
⭐
966
ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.
Phyloseq
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520
phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:
Snapatac
⭐
227
Analysis Pipeline for Single Cell ATAC-seq
Smudgeplot
⭐
200
Inference of ploidy and heterozygosity structure using whole genome sequencing data
Splatter
⭐
195
Simple simulation of single-cell RNA sequencing data
Minion_qc
⭐
174
Quality control for MinION sequencing data
Sccatch
⭐
171
Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
Genomics
⭐
154
A collection of scripts and notes related to genomics and bioinformatics
Ngstools
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142
Programs to analyse NGS data for population genetics purposes
Rnaseq Workflow
⭐
133
A repository for setting up a RNAseq workflow
Decontam
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122
Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data
Facets
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119
Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.
Purecn
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114
Copy number calling and variant classification using targeted short read sequencing
Ancombc
⭐
87
Differential abundance (DA) and correlation analyses for microbial absolute abundance data
Clonevol
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87
Inferring and visualizing clonal evolution in multi-sample cancer sequencing
Basics
⭐
81
BASiCS: Bayesian Analysis of Single-Cell Sequencing Data. This is an unstable experimental version. Please see http://bioconductor.org/packages/BASiCS/ for the official release version
Ichorcna
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73
Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.
Stitch
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67
STITCH - Sequencing To Imputation Through Constructing Haplotypes
Canopy
⭐
55
Accessing Intra-Tumor Heterogeneity and Tracking Longitudinal and Spatial Clonal Evolutionary History by Next-Generation Sequencing.
Tenx
⭐
53
Pipelines for the analysis of 10x single-cell RNA-sequencing data
Cnview
⭐
50
Visualization and annotation of CNVs from population-scale whole-genome sequencing data
Dmrseq
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47
R package for Inference of differentially methylated regions (DMRs) from bisulfite sequencing
Rna Seq Diff Exprn
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44
RNA-Sequencing data differential expression analysis pipeline. Performs: genome coverage (via bedtools and HTSeq), generates Circos code and plots, differential expression (via DESeq and NOISeq), structural variant detection (e.g. fusion genes, via SVDetect) and differential exon usage (via DEXSeq).
Metagenomeseq
⭐
43
Statistical analysis for sparse high-throughput sequencing
Needlestack
⭐
39
Multi-sample somatic variant caller
Spatialexperiment
⭐
38
Mapdamage
⭐
37
mapDamage: tracking and quantifying damage patterns in ancient DNA sequences
Rhea
⭐
36
A set of R scripts for the analysis of microbial profiles
Clusterexperiment
⭐
36
R package of techniques for comparing clusterings of single-cell sequencing data
Msisensor2
⭐
33
Microsatellite instability (MSI) detection for tumor only data.
Qdnaseq
⭐
33
QDNAseq package for Bioconductor
Rca
⭐
30
R package for robust clustering of single cell RNA sequencing data
Codex2
⭐
29
Full-spectrum copy number variation detection by high-throughput DNA sequencing
Codaseq
⭐
29
Functions for compositional analysis of high throughput sequencing
Microbiomeutilities
⭐
29
The is mostly a wrapper tool using phyloseq and microbiome R packages.
Wiggleplotr
⭐
28
A small R package to make sequencing read coverage plots in R.
Shallowhrd
⭐
28
This method uses shallow Whole Genome Sequencing (sWGS) and the segmentation of a genomic profile to assess the Homologous Recombination Deficiency of a tumor based on the number of Large-scale Genomic Alterations (LGAs).
Deepstats
⭐
27
deepStats: a stastitical toolbox for deeptools and genomic signals
Ngs Filters
⭐
25
Filters for false-positive mutation calls in NGS
Readdepth
⭐
24
R package for inferring copy number from read depth
Ngstools
⭐
23
My own tools code for NGS data analysis (Next Generation Sequencing)
Exomepeak2
⭐
23
Peak calling and differential methylation for MeRIP-Seq
Polyrad
⭐
22
Genotype Calling with Uncertainty from Sequencing Data in Polyploids 🍌🍓🥔🍠🥝
Cacao
⭐
22
Callable Cancer Loci - assessment of sequencing coverage for actionable and pathogenic loci in cancer
Aceseqworkflow
⭐
22
Allele-specific copy number estimation with whole genome sequencing
Gnomad Sv Pipeline
⭐
22
Code and custom scripts relevant to gnomAD-SV (Collins*, Brand*, et al., 2020)
Atacseqqc
⭐
22
ATAC-seq Quality Control
Popsv
⭐
22
Population-based detection of structural variation from High-Throughput Sequencing.
Chetah
⭐
21
scRNA-seq cell type identification
Ezrun
⭐
21
An R meta-package for the analysis of Next Generation Sequencing data
Exstra
⭐
20
Expanded STR algorithm for Illumina sequencing data
Methylcc
⭐
20
R/BioC package to estimate the cell composition of whole blood in DNA methylation samples in microarray or sequencing platforms
Updog
⭐
20
Flexible Genotyping of Polyploids using Next Generation Sequencing Data
Lcwgs Guide Tutorial
⭐
19
Kgd
⭐
19
Kinship (genetic relatedness) using GBS (genotyping-by-sequencing) with Depth adjustment
Djvdj
⭐
19
An R package to analyze single-cell V(D)J data
Bioc_2020_tidytranscriptomics
⭐
18
Workshop on tidytranscriptomics: Performing tidy transcriptomics analyses with tidybulk, tidyverse and tidyheatmap
Frmatch
⭐
18
Cell type matching in single-cell RNA-sequencing data using FR-Match
Copenhagen
⭐
17
Analysis of genotyping and next-generation sequencing data in medical and population genetics
Ctdnatools
⭐
17
R package to work with ctDNA sequencing data
Jams_bw
⭐
17
Just a Microbiology System (JAMS) - a suite for analyzing microbiological sequencing data for use on NIH HPC systems (Biowulf)
Subseq
⭐
16
Subsampling of high-throughput sequencing count data
Scdna_myeloid
⭐
16
Processing scripts for single cell DNA sequencing on the Tapestri platform
Mocaseq
⭐
16
Analysis pipelines for cancer genome sequencing in mice.
Kineticstools
⭐
16
Tools for detecting DNA modifications from single molecule, real-time sequencing data
Icnv
⭐
15
Integrated copy number variation detection toolset
Rs
⭐
15
rs - the Racket Sequencer
Ngstk
⭐
15
A toolkit developed by JhuangLab members to facilitate the analysis of next-generation sequencing (NGS) data.
Scale
⭐
15
Allele-Specific Expression by Single-Cell RNA Sequencing
Miracum Pipe
⭐
14
Whole exome sequencing pipeline including advanced variant annotation features and automated PDF reporting.
Copywriter
⭐
14
DNA copy number detection from off-target sequence data
Scmut
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13
Celltagr
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13
This repository contains the CellTag data analysis R package to support clone calling and lineage reconstruction.
Angsd Wrapper
⭐
13
Utilities for analyzing next generation sequencing data.
Deepsnv
⭐
13
The official repository for the deepSNV bioconductor packages. Branch master tracks the official Bioconductor development branch.
Cnaclinic
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13
Kgp
⭐
12
1000 Genomes Project Metadata R Package
Isop
⭐
12
Isoform-level expression patterns in single-cell RNA-sequencing data
Drimpute
⭐
12
Imputing dropout events in single-cell RNA-sequencing data
Assigner
⭐
12
Population assignment analysis using R
Microdecon
⭐
12
An R package for removing contamination from metabarcoding (e.g., microbiome) datasets post-sequencing
Superseq
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12
Assessing the increase in power from increasing read depth in a given RNA-Seq study
Methyliftover
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12
A utility to map bisulfite sequencing data to the Illumina 450K methylation CpG set
Scope
⭐
11
Single-cell COPy number Estimation
Genopheno Catalogshiny
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11
Shiny app for geno-pheno catalog
Aneufinder
⭐
11
Find CNVs in single cell sequencing data.
Normr
⭐
11
Normalization and difference calling for Next Generation Sequencing (NGS) data via joint multinomial modeling.
Bpsc
⭐
11
Beta-Poisson model for single-cell RNA-seq data analyses
Imonitor
⭐
11
This script use to analyze the immune repertoire sequenced by high throughtput sequencing
Dendro
⭐
11
Genetic Heterogeneity Profiling by Single Cell RNA Sequencing
Nucleosome_ctdna
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11
Inferring expressed genes by whole-genome sequencing of plasma DNA
Computel
⭐
10
Compute mean telomere length from Whole Genome Sequencing data.
Antler
⭐
10
R package for single-cell RNA-sequencing analysis
Humanliver
⭐
10
R Data: Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations
Dasper
⭐
10
Detecting Aberrant Splicing Events from RNA-sequencing data
Mrmosaic
⭐
9
MrMosaic (Genomic Mosaic Structural Variant Caller)
Hmp16sdata
⭐
9
16S rRNA Sequencing Data from the Human Microbiome Project
Pancreas_ductal_scrnaseq
⭐
9
The following repository contains code for all scRNAseq analysis and visualization performed in the paper: Single cell resolution analysis of the human pancreatic ductal progenitor cell niche
Scrnaseq Sscs
⭐
9
Identified novel mouse spermatogenesis biomarkers based on single-cell RNA sequencing data
Preseqr
⭐
9
An R package for estimating library complexity
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