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
Contents:
- 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
- CSCD - Cancer-specific circular RNAs database
- AtCircDB
- CircNet
- circBase
- circRNADb
- exoRBase
- EVLncRNAs
- BWA
- STAR
- TMAP
- NovoAlign
- GMAP
- bowtie
- bowtie2
- tophat2
- hisat2
- Edean
- ABySS
- SSAHA2
- oases
- Velvet
- Trinity
- MapSplice2
- RUM
- MECAT
- GATK
- MuTect
- lofreq
- VarScan2
- freebayes
- TVC
- SomaticSniper
- speedseq
- FusionCatcher
- svtoolkit
- pindel
- breakdancer
- delly
- CNVkit
- speedseq
- GRIDSS
- PancanQTL
- TumorFusions
- SVScore
- SVTools
- RDDpred
- iseq
- deepvariant
- SV2
- biopython
- IRanges
- org.Hs.eg.db
- Biobase
- GenomicAlignments
- GenomicRanges
- Rsamtools
- jvarkit
- htslib
- samtools
- bedtools
- vcftools
- bcftools
- bamtools
- bamUtil
- vcflib
- samstat
- seqtk
- sratools
- bcl2fastq2
- ucsc_utils
- MeQA
- IdCheck
- SAMBLASTER
- ngstk
- BioInstaller
- ChromHMM
- 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
- 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