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biopet-bamstats
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public |
BamStats is a package that contains tools to generate stats from a BAM file, merge those stats for multiple samples, and validate the generated stats files.
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2023-06-16 |
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bioconductor-abaenrichment
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public |
Gene expression enrichment in human brain regions
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2023-06-16 |
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biopet-scatterregions
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public |
This tool breaks a reference or bed file into smaller scatter regions of equal size.
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2023-06-16 |
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bioconductor-rnaither
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public |
Statistical analysis of high-throughput RNAi screens
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2023-06-16 |
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bioconductor-cancerinsilico
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public |
An R interface for computational modeling of tumor progression
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2023-06-16 |
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bioconductor-linc
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public |
co-expression of lincRNAs and protein-coding genes
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2023-06-16 |
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bioconductor-m3d
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public |
Identifies differentially methylated regions across testing groups
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2023-06-16 |
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r-poppr
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public |
An R package for genetic analysis of populations with mixed (clonal/sexual) reproduction
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2023-06-16 |
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bioconductor-gofunction
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public |
GO-function: deriving biologcially relevant functions from statistically significant functions
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2023-06-16 |
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bioconductor-genoset
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public |
A RangedSummarizedExperiment with methods for copy number analysis
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2023-06-16 |
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bioconductor-dmrcate
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public |
Methylation array and sequencing spatial analysis methods
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2023-06-16 |
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r-sequenza
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public |
Tools to analyze genomic sequencing data from paired normal-tumor samples, including cellularity and ploidy estimation; mutation and copy number (allele-specific and total copy number) detection, quantification and visualization.
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2023-06-16 |
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ctat-mutations
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public |
Mutation detection in RNA-Seq using GATK-v4.0 in RNA-Seq variant calling, several sources of variant annotation, and filtering based on CRAVAT.
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2023-06-16 |
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r-polysat
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public |
A collection of tools to handle microsatellite data of any ploidy (and samples of mixed ploidy) where allele copy number is not known in partially heterozygous genotypes.
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2023-06-16 |
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assembly-scan
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public |
Assembly summary statistics in JSON format
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2023-06-16 |
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evofold2
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public |
Identifies functional RNA-structure in multiple sequence alignments.
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2023-06-16 |
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translate-gard
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public |
Converts HyPhy 2.3.2 GARD output to JSON
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2023-06-16 |
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connectome-workbench
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public |
Connectome Workbench is an open source, freely available visualization and discovery tool used to map neuroimaging data, especially data generated by the Human Connectome Project
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2023-06-16 |
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bioconductor-dsimer
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public |
dSimer is an R package which provides computation of nine methods for measuring disease-disease similarity, including a standard cosine similarity measure and eight function-based methods. The disease similarity matrix obtained from these nine methods can be visualized through heatmap and network. Biological data widely used in disease-disease associations study are also provided by dSimer.
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2023-06-16 |
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bioconductor-svaplsseq
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public |
SVAPLSseq-An R package to estimate the hidden factors of unwanted variability and adjust for them to enable a more powerful and accurate differential expression analysis based on RNAseq data
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2023-06-16 |
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tiptoft
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public |
Predict plasmids from uncorrected long read data.
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2023-06-16 |
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fred2
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public |
Python-based framework for computational immunomics.
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2023-06-16 |
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slicedimage
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public |
Python module to access sliced imaging data
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2023-06-16 |
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bioconductor-ppidata
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public |
A package that contains the bait to prey directed graphs for protein-protein interactions
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2023-06-16 |
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r-gpca
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public |
This package implements guided principal components analysis for the detection of batch effects in high-throughput data.
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2023-06-16 |
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bioconductor-htseqtools
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public |
We provide efficient, easy-to-use tools for High-Throughput Sequencing (ChIP-seq, RNAseq etc.). These include MDS plots (analogues to PCA), detecting inefficient immuno-precipitation or over-amplification artifacts, tools to identify and test for genomic regions with large accumulation of reads, and visualization of coverage profiles.
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2023-06-16 |
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bioconductor-diffloop
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public |
Identifying differential DNA loops from chromatin topology data
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2023-06-16 |
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any2fasta
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public |
Convert various sequence formats to FASTA
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2023-06-16 |
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bioconductor-findmyfriends
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public |
Microbial Comparative Genomics in R
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2023-06-16 |
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kodoja
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public |
Kodoja: identifying viruses from plant RNA sequencing data
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2023-06-16 |
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stream
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public |
STREAM-Single-cell Trajectories Reconstruction, Exploration And Mapping
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2023-06-16 |
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rapid
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public |
Read Alignment, Analysis, and Differential Pipeline (RAPID) is a set of tools for the alignment, and analysis of genomic regions with small RNA clusters derived from small RNA sequencing data.
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2023-06-16 |
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seer
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public |
sequence element (kmer) enrichment analysis
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2023-06-16 |
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card_trick
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public |
Utility package to find gene <-> drug relationships within CARD
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2023-06-16 |
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r-pegas
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public |
Functions for reading, writing, plotting, analysing, and manipulating allelic and haplotypic data, including from VCF files, and for the analysis of population nucleotide sequences and micro-satellites including coalescent analyses, linkage disequilibrium, population structure (Fst, Amova) and equilibrium (HWE), haplotype networks, minimum spanning tree and network, and median-joining networks.
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2023-06-16 |
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bioconductor-kimod
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public |
A k-tables approach to integrate multiple Omics-Data
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2023-06-16 |
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bioconductor-brainstars
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public |
query gene expression data and plots from BrainStars (B*)
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2023-06-16 |
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bioconductor-sigar
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public |
Statistics for Integrative Genomics Analyses in R
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2023-06-16 |
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openslide-python
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public |
Python interface to OpenSlide
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2023-06-16 |
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r-phytools
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public |
Phylogenetic tools for comparative biology
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2023-06-16 |
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vcfsamplecompare
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public |
This script sorts and (optionally) filters the rows/variants of a VCF file (containing data for 2 or more samples) based on the differences in the variant data between samples or sample groups. Degree of "difference" is determined by either the best possible degree of separation of sample groups by genotype calls or the difference in average allelic frequency of each sample or sample group (with a gap size threshold). The pair of samples or sample groups used to represent the difference for a variant row is the one leading to the greatest difference in consistent genotype or average allelic frequencies (i.e. observation ratios, e.g. AO/DP) of the same variant state. If sample groups are not specified, the pair of samples leading to the greatest difference is greedily discovered and chosen to represent the variant/row.
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2023-06-16 |
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bioconductor-genrank
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public |
Candidate gene prioritization based on convergent evidence
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2023-06-16 |
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bioconductor-dexus
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public |
DEXUS - Identifying Differential Expression in RNA-Seq Studies with Unknown Conditions or without Replicates
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2023-06-16 |
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bioconductor-chipxpressdata
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public |
ChIPXpress Pre-built Databases
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2023-06-16 |
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dca
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public |
Count autoencoder for scRNA-seq denoising
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2023-06-16 |
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bioconductor-encodexplorer
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public |
A compilation of ENCODE metadata
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2023-06-16 |
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gemma
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public |
Linear mixed models (LMMs) for genome-wide association (GWA)
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2023-06-16 |
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pb-assembly
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public |
Meta-package for Falcon/Unzip tool-suite (originally by Jason Chin)
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2023-06-16 |
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taxator-tk
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public |
Taxator-tk sequence taxonomic annotaion
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2023-06-16 |
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r-seqminer
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public |
Integrate sequencing data (Variant call format, e.g. VCF or BCF) or meta-analysis results in R. This package can help you (1) read VCF/BCF files by chromosomal ranges (e.g. 1:100-200); (2) read RareMETAL summary statistics files; (3) read tables from a tabix-indexed files; (4) annotate VCF/BCF files; (5) create customized workflow based on Makefile.
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2023-06-16 |
