Abstract: A curated list of resources for learning bioinformatics. Some of this repo resources were collected by BioInstaller project. You can use BioInstaller to directly download the source code or database files, or fetch the meta information by BioInstaller::get.meta()$item
.
Purpose:
- Provide some of bioinformatics learning resources for beginners
- Provide a profiling of bioinformatics
Field:
- Next generation sequencing (NGS)
- Bioinformatics Data Analysis
Table of content
- Nature Method
- Nature Genetics
- Bioinformatics
- BMC Bioinformatics
- Nucleic Acids Research
- Genome Research
This section mainly copied from enseqlopedia.
Thanks this work: Hadfield, J. & Retief, J. A profusion of confusion in NGS methods naming. Nat Methods 15, 7-8 (2018).
- CEL-Seq
- CirSeq
- CLaP
- CytoSeq
- Digital RNA Sequencing
- DP-Seq
- Drop-Seq
- Hi-SCL
- InDrop
- MARS-Seq
- Nuc-Seq
- PAIR
- Quartz-Seq
- scM&T-Seq
- SCRB-Seq
- scRNA-Seq
- scTrio-seq
- Smart-Seq
- Smart-Seq2
- snRNA-Seq
- STRT-Seq
- SUPeR-Seq
- TCR-LA-MC PCR
- TIVA
- UMI
- 5C
- Div-Seq
- FRISCR
- TCR Chain Pairing
- AbPair
- 2P-Seq
- 3'NT Method
- 3P-Seq
- 3Seq
- 3′-Seq
- 5′-GRO-Seq
- BruChase-Seq
- BruDRB-Seq
- Bru-Seq
- CAGE
- CHART
- ChIRP
- ClickSeq
- GRO-seq
- NET-Seq
- PAL-Seq
- PARE-Seq
- PEAT
- PRO-Cap
- PRO-Seq
- RAP
- RARseq
- RASL-Seq
- RNA-Seq
- SMORE-Seq
- TAIL-Seq
- TATL-Seq
- TIF-Seq
- TL-Seq
- 4sUDRB-Seq
- CaptureSeq
- cP-RNA-Seq
- FRT-Seq
- GMUCT
- mNET-Seq
- AGO-CLIP
- CLASH
- CLIP-Seq or HITS-CLIP
- DLAF
- eCLIP
- hiCLIP
- iCLIP
- miR-CLIP
- miTRAP
- PAR-CLIP
- PIP-Seq
- Pol II CLIP
- RBNS
- Ribo-Seq or ARTSeq
- RIP-Seq
- TRAP-Seq
- TRIBE
- BrdU-CLIP
- HiTS-RAP
- irCLIP
- 2b-RAD
- CPT-seq
- ddRADseq
- Digenome-seq
- EC-seq
- hyRAD
- RAD-Seq
- Rapture
- RC-Seq
- Repli-Seq
- SLAF-seq
- TC-Seq
- Tn-Seq/INSeq
- Bubble-Seq
- NSCR
- NS-Seq
- Rep-Seq/Ig-Seq/MAF
- DNaseI Seq or DNase-Seq
- Pu-seq
- 3-C/Capture-C/Hi-C
- 4C-seq
- 5C
- ATAC-Seq/Fast-ATAC
- CATCH_IT
- Chem-seq
- ChIA-PET
- ChIPmentation
- ChIP-Seq/HT-ChIP/ChIP-exo/Mint-ChIP
- DamID
- DNase I SIM
- FAIRE-seq/Sono-Seq
- FiT-Seq
- HiTS-FLIP
- MINCE-seq
- MNase-Seq/MAINE-Sequcleo-Sequc-seq
- MPE-seq
- NG Capture-C
- NOMe-Seq
- ORGANIC
- PAT-ChIP
- PB_seq
- SELEX or SELEX-seq / HT-SELEX
- THS-seq
- UMI-4C
- X-ChIP-seq
- Aba-seq
- BisChIP-Seq/ChIP-BS-Seq/ChIP-BMS
- BSAS
- BSPP
- BS-Seq/Bisulfite-Seq/WGBS
- CAB-Seq
- EpiRADseq
- fCAB-seq
- fC-CET
- fC-Seal
- hMeDIP-seq
- JBP1-seq
- MAB-seq
- MBDCap-seq/MethylCap-Seq/MiGS
- MeDIP-Seq/DIP-seq
- MIRA
- MRE-Seq and Methyl-Seq
- xBS-Seq
- PBAT
- redBS-Seq/caMAB-seq
- RRBS-Seq
- RRMAB-seq
- TAB-Seq
- TAmC-Seq
- T-WGBS
- Safe-SeqS
- scAba-seq
- scATAC-Seq (Cell index variation)
- scATAC-Seq (Microfluidics variation)
- scBS-Seq
- scM&T-Seq
- scRC-Seq
- SMDB
- smMIP
- G&T-Seq
- 5C
- DR-Seq
- G&T-Seq
- MALBAC
- MDA
- MIDAS/IMS-MDA/ddMDA
- scM&T-Seq
- Drop-ChIP/scChIP-seq
- Duplex-Seq
- MIPSTR
- nuc-seq/SNES
- OS-Seq
- UCSC
- NCBI
- ExPASy
- EMBL-EBI
- TCGA
- COSMIC
- St. Jude PeCan Data Portal
- BIG Data Center
- DAVID Bioinformatics Resources
- cBioPortal
- Oncotator
- QIAGEN Analysis Platform
- Wordcloud
- Omictools
- iCoMut
- UniProt
- Pfam
- SMART
- STRING
- DiseaseEnhancer
- SEECancer
- eQTL Browser
- Cistrome Project
- VarCards
- superdrug2
- MeDReaders
- ECOdrug
- rSNPBase3.0
- MNDR
- MSDD
- funcoup
- proteinatlas
- DGIdb
- Drugbank
- InterPro
- ncbi-biosystems
- denovo-db
- The Human Phenotype Ontology (HPO)
- FANTOM
- dbNSFP
- regSNP-intron
- RADAR
- DARNED
- REDIportal
- LNCediting
- EggNOG
- MiSTIC
- DTMiner
- PDBFlex
- Cancer3d
- Dsysmap
- CBS Prediction Servers
- BWA
- STAR
- TMAP
- NovoAlign
- GMAP
- bowtie
- bowtie2
- tophat2
- hisat2
- Edean
- ABySS
- SSAHA2
- oases
- Velvet
- Trinity
- MapSplice2
- RUM
- MECAT
- DART
- rHAT
- taxmaps: large DNA/RNA metagenomics samples
- MARVEL: consists of a set of tools that facilitate the overlapping, patching, correction and assembly of noisy (not so noisy ones as well) long reads.
- GATK
- MuTect
- lofreq
- VarScan2
- freebayes
- TVC
- SomaticSniper
- speedseq
- FusionCatcher
- svtoolkit
- pindel
- breakdancer
- delly
- CNVkit
- speedseq
- GRIDSS
- PancanQTL
- TumorFusions
- SVScore
- SVTools
- RDDpred
- iseq
- deepvariant
- SV2
- facets
- MutScan
- svaba: structural variation and indel detection by local assembly
- manta: structural variant and indel caller using mapped sequencing data
- JAFFA: a multi-step pipeline that takes either raw RNA-Seq reads, or pre-assembled transcripts, then searches for gene fusions
- Picky: structural variants pipeline for long reads
- CREST: a algorithm for detecting genomic structural variations at base-pair resolution using next-generation sequencing data
- Control-FREEC: a tool for detection of copy-number changes and allelic imbalances (including LOH) using deep-sequencing data
- Strelka: accurate somatic small-variant calling from sequenced tumor–normal sample pairs
- ANNOVAR
- SnpEff
- gemini
- VEP
- Variant Annotation Integrator
- vcfanno
- pcgr
- annovarR
- OncodriveCLUST: exploiting the positional clustering of somatic mutations to identify cancer genes
- ProteinPaint
- AGFusion
- GenomeUPlot
- BreakPointSurveyor
- chimeraviz
- Oncoprinter
- MutationMapper
- pv: 3D structure visualization in WEB
- g2s: mappings between protein sequence positions and PDB 3D protein structure models
- NGB: structural Variations (SVs) visualization capabilities, high performance, scalability, and cloud data support
- viral-ngs
- qap
- ROP: discovering the source of all RNA-seq reads, including those originating from repeat sequences, recombinant B and T cell receptors, and microbial communities
- seurat
- SCnorm
- dropClust
- scran: batch effect adjust
- trendsceek: spatial expression trends in single-cell gene expression data
- scRNA-tools: a database of software tools for the analysis of single-cell RNA-seq data.
- awesome-single-cell: list of software packages (and the people developing these methods) for single-cell data analysis, including RNA-seq, ATAC-seq, etc.
- biopython
- IRanges
- org.Hs.eg.db
- Biobase
- GenomicAlignments
- GenomicRanges
- Rsamtools
- jvarkit
- htslib
- samtools
- bedtools
- vcftools
- bcftools
- bamtools
- maftools
- bamUtil
- vcflib
- samstat
- seqtk
- sratools
- bcl2fastq2
- ucsc_utils
- MeQA
- IdCheck
- SAMBLASTER
- ngstk
- BioInstaller
- ChromHMM
- ABSOLUTE
- HAPSEG
- Atlas-SNP, Atlas2 Suite
- Beagle
- CIBERSORT
- biobloom
- APAtrap
- phenopredict: predicting phenotype sample information using gene expression
- recount
- bart: predicting functional transcription factors using gene set or a ChIP-seq dataset as input
- LSMM (Latent Sparse Mixed Model): integrating functional annotations with genome-wide association studies
- medcalc
- GraphPad
- ImageJ
- SPSS
- R
- gvmap
- easySVG
- hexmapr
- clustergrammer
- chromVAR
- echarts
- plotly
- qvalue: estimating q-values and false discovery rate quantities
- GenVisR: genome data visualizations
- r-color-palettes: Comprehensive list of color palettes available in r
- sequenza: a novel set of tools providing a fast python script to genotype cancer samples, and an R package to estimate cancer cellularity, ploidy, genome wide copy number profile and infer for mutated alleles.
- Teamviewer
- Sunlogin
- Splashtop
- Chrome Remote Desktop app
- Logmein
- PC Anywhere
- GoToMyPC
- Radmin
- UltraVNC
- R packages
- stringr
- Bioconductor Tutorial
- limma
- 30分钟学会ggplot2
- R Graphics Cookbook
- Introduction to data.table
- RSQLite
- R Graphics
- Wordcloud2
- SPSS Beginners Tutorials
- 维基百科 - K-Means聚类算法
- 维基百科 - KNN算法
- 维基百科 - SVM算法
- 维基百科 - HMM模型
- 维基百科 - KNN算法
- STAT115课程 - HMM算法PPT
- 机器学习常用算法
- 机器学习资源列表
- Review:Deep learning, genomics, and precision medicine
- 华大基因生物信息学培训教材
- 生物信息学入门
- 《生物信息学入门最佳实践》
- The Biostar Handbook: A Beginner's Guide to Bioinformatics
- Bioinformatics Data Skills
- 生信菜鸟团博客
- 生信技能树论坛