Topic · Research & Science
Best bioinformatics skills, page 23
Bioinformatics skills, ranked
Ranked by score. Sort bymost stars,trending,newest,recently updated
| # | Skill | Repository | Stars | Used in | Tokens | Auto-check | Licence | Updated |
|---|---|---|---|---|---|---|---|---|
| 1057 | This package encapsulate many functions to conduct a differential topology analysis. | bioMate-AI/ | 804 | — | ~1.6k | Automated safety check: Pass | Unknown | 3 mo ago |
| 1058 | 1058.Bioconductor Cotan Statistical and computational method to analyze the co-expression of gene pairs at single cell level. | bioMate-AI/ | 804 | — | ~1.7k | Automated safety check: Pass | Unknown | 3 mo ago |
| 1059 | Provides S4 classes for general nucleases, CRISPR nucleases, CRISPR nickases, and base editors.Several CRISPR-specific genome arithmetic functions are implemented to help extract genomic coordinates… | bioMate-AI/ | 804 | — | ~1.5k | Automated safety check: Pass | Unknown | 3 mo ago |
| 1060 | Provides a comprehensive suite of functions to design and annotate CRISPR guide RNA (gRNAs) sequences. | bioMate-AI/ | 804 | — | ~1.2k | Automated safety check: Pass | Unknown | 3 mo ago |
| 1061 | Provides R wrappers of several on-target and off-target scoring methods for CRISPR guide RNAs (gRNAs). | bioMate-AI/ | 804 | — | ~1.9k | Automated safety check: Pass | Unknown | 3 mo ago |
| 1062 | Provides functionalities to visualize and contextualize CRISPR guide RNAs (gRNAs) on genomic tracks across nucleases and applications. | bioMate-AI/ | 804 | — | ~1.3k | Automated safety check: Pass | Unknown | 3 mo ago |
| 1063 | 1063.Bioconductor Cytomem MEM, Marker Enrichment Modeling, automatically generates and displays quantitative labels for cell populations that have been identified from single-cell data. | bioMate-AI/ | 804 | — | ~1.5k | Automated safety check: Pass | Unknown | 3 mo ago |
| 1064 | 1064.Bioconductor Deconvr This package provides a collection of functions designed for analyzing deconvolution of the bulk sample(s) using an atlas of reference omic signature profiles and a user-selected model. | bioMate-AI/ | 804 | — | ~1.5k | Automated safety check: Pass | Unknown | 3 mo ago |
| 1065 | A package for demultiplexing single-cell sequencing experiments of pooled cells labeled with barcode oligonucleotides. | bioMate-AI/ | 804 | — | ~1.5k | Automated safety check: Pass | Unknown | 3 mo ago |
| 1066 | 1066.Bioconductor Deseq2 Uses DESeq2 to estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution. | bioMate-AI/ | 804 | — | ~4.8k | Automated safety check: Pass | Unknown | 3 mo ago |
| 1067 | 1067.Bioconductor Despace Intuitive framework for identifying spatially variable genes (SVGs) via edgeR, a popular method for performing differential expression analyses. | bioMate-AI/ | 804 | — | ~1.6k | Automated safety check: Pass | Unknown | 3 mo ago |
| 1068 | 1068.Bioconductor Dexma performing all the steps of gene expression meta-analysis considering the possible existence of missing genes. | bioMate-AI/ | 804 | — | ~1.6k | Automated safety check: Pass | Unknown | 3 mo ago |
| 1069 | 1069.Bioconductor Dino Dino normalizes single-cell, mRNA sequencing data to correct for technical variation, particularly sequencing depth, prior to downstream analysis. | bioMate-AI/ | 804 | — | ~1.6k | Automated safety check: Pass | Unknown | 3 mo ago |
| 1070 | doubletrouble aims to identify duplicated genes from whole-genome protein sequences and classify them based on their modes of duplication. | bioMate-AI/ | 804 | — | ~914 | Automated safety check: Pass | Unknown | 3 mo ago |
| 1071 | The filtering uses intelligent methods to generate output 10X matrices as would be otherwise generated by CellRanger. | bioMate-AI/ | 804 | — | ~4.2k | Automated safety check: Pass | Unknown | 3 mo ago |
| 1072 | Provides utilities for identifying drug-target interactions for sets of small molecule or gene/protein identifiers. | bioMate-AI/ | 804 | — | ~1.2k | Automated safety check: Pass | Unknown | 3 mo ago |
| 1073 | 1073.Bioconductor Easier This package provides a workflow for the use of EaSIeR tool, developed to assess patients' likelihood to respond to ICB therapies providing just the patients' RNA-seq data as input. | bioMate-AI/ | 804 | — | ~1.9k | Automated safety check: Pass | Unknown | 3 mo ago |
| 1074 | 1074.Bioconductor Edger Estimates differential gene expression for short read sequence count using methods appropriate for count data. | bioMate-AI/ | 804 | — | ~3k | Automated safety check: Pass | Unknown | 3 mo ago |
| 1075 | Epialleles are specific DNA methylation patterns that are mitotically and/or meiotically inherited. | bioMate-AI/ | 804 | — | ~1.7k | Automated safety check: Pass | Unknown | 3 mo ago |
| 1076 | epigraHMM provides a set of tools for the analysis of epigenomic data based on hidden Markov Models. | bioMate-AI/ | 804 | — | ~1.7k | Automated safety check: Pass | Unknown | 3 mo ago |
| 1077 | The epistack package main objective is the visualizations of stacks of genomic tracks (such as, but not restricted to, ChIP-seq, ATAC-seq, DNA methyation or genomic conservation data) centered at… | bioMate-AI/ | 804 | — | ~2.4k | Automated safety check: Pass | Unknown | 3 mo ago |
| 1078 | 1078.Bioconductor Escher The creation of effective visualizations is a fundamental component of data analysis. | bioMate-AI/ | 804 | — | ~1.7k | Automated safety check: Pass | Unknown | 3 mo ago |
| 1079 | This package builds on existing tools and adds some simple but extremely useful capabilities for working wth ChIP-Seq data. | bioMate-AI/ | 804 | — | ~1.2k | Automated safety check: Pass | Unknown | 3 mo ago |
| 1080 | 1080.Bioconductor Findit2 This package implements functions to find influential TF and target based on different input type. | bioMate-AI/ | 804 | — | ~1.2k | Automated safety check: Pass | Unknown | 3 mo ago |
| 1081 | 1081.Bioconductor Gatom This package implements a metabolic network analysis pipeline to identify an active metabolic module based on high throughput data. | bioMate-AI/ | 804 | — | ~1.7k | Automated safety check: Pass | Unknown | 3 mo ago |
| 1082 | This package contain functions to run genomic instability analysis (GIA) from scRNA-Seq data. | bioMate-AI/ | 804 | — | ~1.6k | Automated safety check: Pass | Unknown | 3 mo ago |
| 1083 | The ability to efficiently represent and manipulate genomic annotations and alignments is playing a central role when it comes to analyzing high-throughput sequencing data (a.k.a. | bioMate-AI/ | 804 | — | ~4.7k | Automated safety check: Pass | Unknown | 3 mo ago |
| 1084 | Gene Expression Omnibus(GEO) and The Cancer Genome Atlas (TCGA) provide us with a wealth of data, such as RNA-seq, DNA Methylation, SNP and Copy number variation data. | bioMate-AI/ | 804 | — | ~2.2k | Automated safety check: Pass | Unknown | 3 mo ago |
| 1085 | 1085.Bioconductor Ggmanh Manhattan plot and QQ Plot are commonly used to visualize the end result of Genome Wide Association Study. | bioMate-AI/ | 804 | — | ~1.3k | Automated safety check: Pass | Unknown | 3 mo ago |
| 1086 | granulator is an R package for the cell type deconvolution of heterogeneous tissues based on bulk RNA-seq data or single cell RNA-seq expression profiles. | bioMate-AI/ | 804 | — | ~1.7k | Automated safety check: Pass | Unknown | 3 mo ago |
| 1087 | An implementation, which takes input data and makes it available for proper batch effect removal by ComBat or Limma. | bioMate-AI/ | 804 | — | ~1.2k | Automated safety check: Pass | Unknown | 3 mo ago |
| 1088 | Systematic 3D interaction calls and differential analysis for Hi-C and HiChIP. | bioMate-AI/ | 804 | — | ~1.3k | Automated safety check: Pass | Unknown | 3 mo ago |
| 1089 | hoodscanR is an user-friendly R package providing functions to assist cellular neighborhood analysis of any spatial transcriptomics data with single-cell resolution. | bioMate-AI/ | 804 | — | ~1.4k | Automated safety check: Pass | Unknown | 3 mo ago |
| 1090 | InterCellar is implemented as an R/Bioconductor Package containing a Shiny app that allows users to interactively analyze cell-cell communication from scRNA-seq data. | bioMate-AI/ | 804 | — | ~985 | Automated safety check: Pass | Unknown | 3 mo ago |
| 1091 | 1091.Bioconductor Limma Given a matrix of counts (e.g. An agent skill from bioMate-AI/biomate-bioconductor-kb. | bioMate-AI/ | 804 | — | ~2.9k | Automated safety check: Pass | Unknown | 3 mo ago |
| 1092 | 1092.Bioconductor Lintind When we combine gene-editing technology and sequencing technology, we need to reconstruct a lineage tree from alleles generated and calculate the similarity between each pair of groups. | bioMate-AI/ | 804 | — | ~1.7k | Automated safety check: Pass | Unknown | 3 mo ago |
| 1093 | lisaClust provides a series of functions to identify and visualise regions of tissue where spatial associations between cell-types is similar. | bioMate-AI/ | 804 | — | ~1.4k | Automated safety check: Pass | Unknown | 3 mo ago |
| 1094 | 1094.Bioconductor Macsr The Model-based Analysis of ChIP-Seq (MACS) is a widely used toolkit for identifying transcript factor binding sites. | bioMate-AI/ | 804 | — | ~890 | Automated safety check: Pass | Unknown | 3 mo ago |
| 1095 | 1095.Bioconductor Mastr mastR is an R package designed for automated screening of signatures of interest for specific research questions. | bioMate-AI/ | 804 | — | ~1.6k | Automated safety check: Pass | Unknown | 3 mo ago |
| 1096 | Data quality assessment is an integral part of preparatory data analysis to ensure sound biological information retrieval. | bioMate-AI/ | 804 | — | ~1.1k | Automated safety check: Pass | Unknown | 3 mo ago |
| 1097 | mirTarRnaSeq R package can be used for interactive mRNA miRNA sequencing statistical analysis. | bioMate-AI/ | 804 | — | ~2k | Automated safety check: Pass | Unknown | 3 mo ago |
| 1098 | Mass spectrometry (MS) data backend supporting import and export of MS/MS library spectra from MassBank record files. | bioMate-AI/ | 804 | — | ~1k | Automated safety check: Pass | Unknown | 3 mo ago |
| 1099 | The MsDataHub package uses the ExperimentHub infrastructure to distribute raw mass spectrometry data files, peptide spectrum matches or quantitative data from proteomics and metabolomics experiments. | bioMate-AI/ | 804 | — | ~1.3k | Automated safety check: Pass | Unknown | 3 mo ago |
| 1100 | 1100.Bioconductor Msnbase MSnbase provides infrastructure for manipulation, processing and visualisation of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data. | bioMate-AI/ | 804 | — | ~3.2k | Automated safety check: Pass | Unknown | 3 mo ago |
| 1101 | Tools for LiP peptide and protein significance analysis. An agent skill from bioMate-AI/biomate-bioconductor-kb. | bioMate-AI/ | 804 | — | ~1.1k | Automated safety check: Pass | Unknown | 3 mo ago |
| 1102 | 1102.Bioconductor Mudata Save MultiAssayExperiments to h5mu files supported by muon and mudata. | bioMate-AI/ | 804 | — | ~1k | Automated safety check: Pass | Unknown | 3 mo ago |
| 1103 | NanoTube includes functions for the processing, quality control, analysis, and visualization of NanoString nCounter data. | bioMate-AI/ | 804 | — | ~966 | Automated safety check: Pass | Unknown | 3 mo ago |
| 1104 | 1104.Bioconductor Nnsvg Method for scalable identification of spatially variable genes (SVGs) in spatially-resolved transcriptomics data. | bioMate-AI/ | 804 | — | ~925 | Automated safety check: Pass | Unknown | 3 mo ago |
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