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bioconductor-chipsim
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public |
Simulation of ChIP-seq experiments
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2023-12-22 |
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bioconductor-ideoviz
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public |
Plots data (continuous/discrete) along chromosomal ideogram
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2023-12-22 |
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bioconductor-chipenrich.data
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public |
Companion package to chipenrich
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2023-12-22 |
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bioconductor-trnascanimport
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public |
Importing a tRNAscan-SE result file as GRanges object
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2023-12-22 |
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bioconductor-hitc
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public |
High Throughput Chromosome Conformation Capture analysis
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2023-12-22 |
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bioconductor-chipanalyser
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public |
ChIPanalyser: Predicting Transcription Factor Binding Sites
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2023-12-22 |
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bioconductor-hiannotator
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public |
Functions for annotating GRanges objects
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2023-12-22 |
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bioconductor-mmdiff2
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public |
Statistical Testing for ChIP-Seq data sets
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2023-12-22 |
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bioconductor-gothic
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public |
Binomial test for Hi-C data analysis
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2023-12-22 |
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bioconductor-starbiotrek
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public |
StarBioTrek
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2023-12-22 |
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bioconductor-cexor
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public |
An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates
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2023-12-22 |
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bioconductor-mira
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public |
Methylation-Based Inference of Regulatory Activity
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2023-12-22 |
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bioconductor-sparsesignatures
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public |
SparseSignatures
|
2023-12-22 |
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bioconductor-cemitool
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public |
Co-expression Modules identification Tool
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2023-12-22 |
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bioconductor-fccac
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public |
functional Canonical Correlation Analysis to evaluate Covariance between nucleic acid sequencing datasets
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2023-12-22 |
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bioconductor-methylseekr
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public |
Segmentation of Bis-seq data
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2023-12-22 |
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bioconductor-sevenc
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public |
Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs
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2023-12-22 |
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bioconductor-excluster
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public |
ExCluster robustly detects differentially expressed exons between two conditions of RNA-seq data, requiring at least two independent biological replicates per condition
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2023-12-22 |
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bioconductor-methylinheritance
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public |
Permutation-Based Analysis associating Conserved Differentially Methylated Elements Across Multiple Generations to a Treatment Effect
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2023-12-22 |
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bioconductor-seqsetvis
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public |
Set Based Visualizations for Next-Gen Sequencing Data
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2023-12-22 |
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bioconductor-bsseqdata
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public |
Example whole genome bisulfite data for the bsseq package
|
2023-12-22 |
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bioconductor-segmentseq
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public |
Methods for identifying small RNA loci from high-throughput sequencing data
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2023-12-22 |
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bioconductor-methinheritsim
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public |
Simulating Whole-Genome Inherited Bisulphite Sequencing Data
|
2023-12-22 |
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bioconductor-snplocs.hsapiens.dbsnp150.grch38
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public |
SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 150. The source data files used for this package were created by NCBI between March 12-14, 2017, and contain SNPs mapped to reference genome GRCh38.p7 (a patched version of GRCh38 that doesn't alter chromosomes 1-22, X, Y, MT). Note that these SNPs can be "injected" in BSgenome.Hsapiens.NCBI.GRCh38 or in BSgenome.Hsapiens.UCSC.hg38.
|
2023-12-22 |
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bioconductor-eatonetalchipseq
|
public |
ChIP-seq data of ORC-binding sites in Yeast excerpted from Eaton et al. 2010
|
2023-12-22 |
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bioconductor-biseq
|
public |
Processing and analyzing bisulfite sequencing data
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2023-12-22 |
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bioconductor-dmchmm
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public |
Differentially Methylated CpG using Hidden Markov Model
|
2023-12-22 |
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bioconductor-snplocs.hsapiens.dbsnp149.grch38
|
public |
SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 149. The source data files used for this package were created by NCBI between November 8-12, 2016, and contain SNPs mapped to reference genome GRCh38.p7 (a patched version of GRCh38 that doesn't alter chromosomes 1-22, X, Y, MT). Note that these SNPs can be "injected" in BSgenome.Hsapiens.NCBI.GRCh38 or in BSgenome.Hsapiens.UCSC.hg38.
|
2023-12-22 |
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bioconductor-beat
|
public |
BEAT - BS-Seq Epimutation Analysis Toolkit
|
2023-12-22 |
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bioconductor-desousa2013
|
public |
Poor prognosis colon cancer is defined by a molecularly distinct subtype and precursor lesion
|
2023-12-22 |
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bioconductor-basecallqc
|
public |
Working with Illumina Basecalling and Demultiplexing input and output files
|
2023-12-22 |
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bioconductor-snplocs.hsapiens.dbsnp144.grch38
|
public |
SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 144. The source data files used for this package were created by NCBI on May 30, 2015, and contain SNPs mapped to reference genome GRCh38.p2 (a patched version of GRCh38 that doesn't alter chromosomes 1-22, X, Y, MT). Note that these SNPs can be "injected" in BSgenome.Hsapiens.NCBI.GRCh38 or in BSgenome.Hsapiens.UCSC.hg38.
|
2023-12-22 |
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bioconductor-ballgown
|
public |
Flexible, isoform-level differential expression analysis
|
2023-12-22 |
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bioconductor-leebamviews
|
public |
leeBamViews -- multiple yeast RNAseq samples excerpted from Lee 2009
|
2023-12-22 |
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bioconductor-snplocs.hsapiens.dbsnp144.grch37
|
public |
SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 144. The source data files used for this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped to reference genome GRCh37.p13. WARNING: Note that the GRCh37.p13 genome is a patched version of GRCh37. However the patch doesn't alter chromosomes 1-22, X, Y, MT. GRCh37 itself is the same as the hg19 genome from UCSC *except* for the mitochondrion chromosome. Therefore, the SNPs in this package can be "injected" in BSgenome.Hsapiens.UCSC.hg19 and they will land at the correct position but this injection will exclude chrM (i.e. nothing will be injected in that sequence).
|
2023-12-22 |
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bioconductor-coverageview
|
public |
Coverage visualization package for R
|
2023-12-22 |
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bioconductor-rtrmui
|
public |
A shiny user interface for rTRM
|
2023-12-22 |
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bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch38
|
public |
Extra SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 144. The source data files used for this package were created by NCBI on May 30, 2015, and contain SNPs mapped to reference genome GRCh38.p2 (a patched version of GRCh38 that doesn't alter chromosomes 1-22, X, Y, MT). While the SNPlocs.Hsapiens.dbSNP144.GRCh38 package contains only molecular variations of class "snp", this package contains molecular variations of other classes (in-del, heterozygous, microsatellite, named-locus, no-variation, mixed, and multinucleotide-polymorphism).
|
2023-12-22 |
|
bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37
|
public |
Extra SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 144. The source data files used for this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped to reference genome GRCh37.p13 (a patched version of GRCh37 that doesn't alter chromosomes 1-22, X, Y, MT). While the SNPlocs.Hsapiens.dbSNP144.GRCh37 package contains only molecular variations of class "snp", this package contains molecular variations of other classes (in-del, heterozygous, microsatellite, named-locus, no-variation, mixed, and multinucleotide-polymorphism).
|
2023-12-22 |
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bioconductor-chromheatmap
|
public |
Heat map plotting by genome coordinate
|
2023-12-22 |
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bioconductor-rsvsim
|
public |
RSVSim: an R/Bioconductor package for the simulation of structural variations
|
2023-12-22 |
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bioconductor-isomirs
|
public |
Analyze isomiRs and miRNAs from small RNA-seq
|
2023-12-22 |
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bioconductor-oppar
|
public |
Outlier profile and pathway analysis in R
|
2023-12-22 |
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bioconductor-coseq
|
public |
Co-Expression Analysis of Sequencing Data
|
2023-12-22 |
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bioconductor-translatome
|
public |
Comparison between multiple levels of gene expression
|
2023-12-22 |
|
bioconductor-slalom
|
public |
Factorial Latent Variable Modeling of Single-Cell RNA-Seq Data
|
2023-12-22 |
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bioconductor-omicrexposome
|
public |
Exposome and omic data associatin and integration analysis
|
2023-12-22 |
|
bioconductor-singscore
|
public |
Rank-based single-sample gene set scoring method
|
2023-12-22 |
|
bioconductor-diffcoexp
|
public |
Differential Co-expression Analysis
|
2023-12-22 |
|
bioconductor-doppelgangr
|
public |
Identify likely duplicate samples from genomic or meta-data
|
2023-12-22 |
