└── README.md


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  1 | # Learn Bioinformatics (Resources)
  2 | Hi There, I always received questions like <b> <i> “Could you please help me to learn Bioinformatics?”  </i> </b> and since this is a general question and you need to specify more which topics you would like to learn so I decided to make this repo and I will update it continuously as I found more resources and materials. I always prefer to point out to English materials as I think they are more professionals and educated but I will mention some materials that I really like in Arabic too. <b> <i> All materials that I mentioned here depends on my personal preferences so it may taste differently to the others </i> </b>.
  3 |   <table>  
  4 |         <thead>
  5 |            <th> Materials & Resources </th>
  6 |            <th> Links </th>
  7 |         </thead>
  8 |         <tr>
  9 |             <td> Genomic Data Science Specialization </td>
 10 |             <td> <li> <a href="https://www.coursera.org/specializations/genomic-data-science"> <b> Link </b></a> </li> </td>
 11 |        </tr>
 12 |           <tr>
 13 |             <td> Ben Langmead YouTube Playlists on Algorithms for DNA Sequencing, <br> Indexing, Sketching and random data structures  </td>
 14 |             <td> <li> <a href="https://www.youtube.com/user/BenLangmead/playlists"> <b> Link </b></a> </li> </td>
 15 |        </tr>
 16 |             <tr>
 17 |             <td> Applied Computational Genomics Course by Aaron Quinlan  </td>
 18 |             <td> <li> <a href="https://github.com/quinlan-lab/applied-computational-genomics"> <b> Link </b></a> </li> </td>
 19 |        </tr>
 20 |        <tr>
 21 |             <td> MIT Deep Learning Genomics by Manolis Kellis   </td>
 22 |             <td> <li> <a href="https://mit6874.github.io/"> <b> Link </b></a> </li> </td>
 23 |        </tr>
 24 |          <tr>
 25 |             <td> Introduction to Bioinformatics and Computational Biology by Xiaole Shirley Liu   </td>
 26 |             <td> <li> <a href="https://liulab-dfci.github.io/bioinfo-combio/"> <b> Link </b></a> </li> </td>
 27 |        </tr>
 28 |           <tr>
 29 |             <td> The Canadian Bioinformatics Workshops   </td>
 30 |             <td> <li> <a href="https://bioinformaticsdotca.github.io/"> <b> Link </b></a> </li> </td>
 31 |        </tr>
 32 |             <tr>
 33 |             <td> Bioinformatics Coach Channel   </td>
 34 |             <td> <li> <a href="https://www.youtube.com/channel/UCOJM9xzqDc6-43j2x_vXqCQ"> <b> Link </b></a> </li> </td>
 35 |        </tr>
 36 |               <tr>
 37 |             <td> C. Titus Brown Blog, Lab Training, Twitter account   </td>
 38 |             <td> <li> <a href="http://ivory.idyll.org/blog/"> <b> Blog Link </b></a> </li>
 39 |                  <li> <a href="https://angus.readthedocs.io/en/2019/"> <b> Training Link </b></a> </li>
 40 |                  <li> <a href="https://dib-training.readthedocs.io/en/pub/"> <b> Training Link </b></a> </li> </td>    
 41 |        </tr>
 42 |          <tr>
 43 |             <td> Micheal Schatz Github Repo  </td>
 44 |             <td> <li> <a href="https://github.com/schatzlab"> <b> Link </b></a> </li> </td>
 45 |        </tr>
 46 |        <tr>
 47 |             <td> Shomu's Bioinformatics with practical (SBWP) (for basics)   </td>
 48 |             <td> <li> <a href="https://www.youtube.com/watch?v=w-uk-_TOgR0&list=PLb0WW0k29aHrF8aZzK17ORTesZsd-lING"> <b> Link </b></a> </li> </td>
 49 |        </tr>
 50 |          <tr>
 51 |             <td> Bioinformatics Data Skills: Reproducible and Robust Research <br> with Open Source Tools by Vince Buffalo   </td>
 52 |             <td> <li> <a href="https://www.amazon.com/Bioinformatics-Data-Skills-Reproducible-Research/dp/1449367372"> <b> Book Link on Amazon </b></a> </li> </td>
 53 |        </tr>
 54 |            <tr>
 55 |             <td> Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins <br> by Andreas D. Baxevanis, Gary D. Bader, and David S. Wishart  </td>
 56 |             <td> <li> <a href="https://www.amazon.com/Bioinformatics-Practical-Guide-Analysis-Proteins/dp/1119335582"> <b> Book Link on Amazon </b></a> </li> </td>
 57 |        </tr>
 58 |              <tr>
 59 |             <td> Biostar Handbook  </td>
 60 |             <td> <li> <a href="https://www.biostarhandbook.com/"> <b> Book Link </b></a> </li> </td>
 61 |        </tr>
 62 |                <tr>
 63 |             <td> Arabic Materials  </td>
 64 |             <td> <li> <a href="https://www.youtube.com/watch?v=GHqKnE6LL5Q&list=PLt0thylmbOcl45ysVO_z9Qw_n63pH1DpP"> <b> Link </b></a> </li> </td>
 65 |        </tr>
 66 |        <tr>
 67 |             <td> Galaxy Training  </td>
 68 |             <td> <li> <a href="https://training.galaxyproject.org/training-material/"> <b> Link </b></a> </li> </td>
 69 |        </tr>
 70 |                  <tr>
 71 |             <td> Telegram Channel for Mansoura University Medical Informatics Students  </td>
 72 |             <td> <li> <a href="https://t.me/+jqTpvLsIh5szNzc0"> <b> Channel Link </b></a> </li> </td>
 73 |        </tr>
 74 |                    <tr>
 75 |             <td> Bioinformatics by Open Source Society University  </td>
 76 |             <td> <li> <a href="https://github.com/ossu/bioinformatics"> <b> Link </b></a> </li> </td>
 77 |        </tr>
 78 |                      <tr>
 79 |             <td> strand-ngs.com  </td>
 80 |             <td> <li> <a href="https://www.strand-ngs.com/files/manual/reference/toc.html"> <b> Link </b></a> </li> </td>
 81 |        </tr>
 82 |          <tr>
 83 |             <td> Introduction to bioinformatics for RNA sequence analysis  </td>
 84 |             <td> <li> <a href="https://rnabio.org/course/"> <b> Link </b></a> </li> </td>
 85 |        </tr>
 86 |          <tr>
 87 |             <td> Informatics for RNA-seq: A web resource for analysis on the cloud  </td>
 88 |             <td> <li> <a href="https://github.com/griffithlab/rnaseq_tutorial"> <b> Link </b></a> </li> </td>
 89 |         </tr>
 90 |         <tr>
 91 |             <td> GaBI Academy: GaBI edX talks/playlists  </td>
 92 |             <td> <li> <a href="https://www.youtube.com/channel/UCOnantUhzNxZxqn_SpIFTJg/playlists"> <b> Link </b></a> </li> </td>
 93 |         </tr>
 94 |           <tr>
 95 |             <td> Learn SeqAn : an open source C++ library of efficient algorithms and data structures </td>
 96 |             <td> <li> <a href="https://seqan.readthedocs.io/en/seqan-v1.4.2/Tutorial.html"> <b> Link </b></a> </li> </td>
 97 |         </tr>
 98 |          <tr>
 99 |             <td> learning vcf file </td>
100 |             <td> <li> <a href="https://github.com/davetang/learning_vcf_file"> <b> Link </b></a> </li> </td>
101 |         </tr>
102 |         <tr>
103 |           <td> Notes on Some Projects Analysis: Assembly, Virant Calling, Metagenomics, and Gene Expresstion </td>
104 |            <td> <li> <a href="https://github.com/njdbickhart/labnotes"> <b> Link </b></a> </li> </td>   
105 |        </tr>
106 |         <tr> 
107 |           <td> E-book by NYU Center For Genomics and Systems Biology (NGS Resources)   </td>
108 |           <td> <li> <a href="https://learn.gencore.bio.nyu.edu/"> <b> Link </b></a> </li> </td>  
109 |         </tr>
110 |         <tr> 
111 |           <td> Metagenomics Wiki   </td>
112 |           <td> <li> <a href="https://www.metagenomics.wiki/pdf"> <b> Link </b></a> </li> </td>  
113 |         </tr>
114 |           <tr>
115 |           <td> Statistical Rethinking   </td>
116 |           <td> <li> <a href="https://xcelab.net/rm/statistical-rethinking/"> <b> Link </b></a> </li> </td>  
117 |         </tr>
118 |           </tr>
119 |           <tr>
120 |           <td> Best practices for bulk and single cell RNA-seq data analysis   </td>
121 |           <td> <li> <a href="https://diytranscriptomics.com/"> <b> Link </b></a> </li> </td>  
122 |         </tr>
123 |           <tr>
124 |           <td> Bitesize Bioiniformatics </td>
125 |           <td> <li> <a href="https://www.youtube.com/watch?v=PPMyvIJJbeg&list=PLbiByRpDb_hP7b-I1GR4eEWCD2OqdZEg1"> <b> Link </b></a> </li> </td>  
126 |           </tr>
127 |            <tr>
128 |              <td> Michael Edwards Playlists of Bioinformatics  </td>
129 |              <td> <li> <a href="https://www.youtube.com/c/MichaelEdwardsbioinfo/playlists"> <b> Link </b></a> </li> </td>  
130 |            </tr>
131 |            <tr>
132 |              <td> Online Tutorials and Webinar Library by EMBL-EBI Training   </td>
133 |              <td> <li> <a href="https://www.ebi.ac.uk/training/on-demand?facets=type:Online%20tutorial"> <b> Link </b></a> </li> </td>  
134 |            </tr>
135 |             <tr>
136 |              <td> Computational Genomics with R   </td>
137 |              <td> <li> <a href="https://compgenomr.github.io/book/"> <b> Link </b></a> </li> </td>  
138 |            </tr>
139 |            <tr>
140 |              <td> Computational Genomics Tutorial: Massey University course </td>
141 |              <td> <li> <a href="https://genomics.sschmeier.com/index.html"> <b> Link </b></a> </li> </td>  
142 |            </tr>
143 |            <tr>
144 |              <td> Chipster Tutorials: Single cell RNA-seq, Variant Calling, Microbial Community Analysis  </td>
145 |              <td> <li> <a href="https://www.youtube.com/c/ChipsterTutorials/playlists"> <b> Link </b></a> </li> </td>  
146 |            </tr>
147 |            <tr>
148 |              <td> The National Library of Medicine playlists: The NCBI Minute Webinars  </td>
149 |              <td> <li> <a href="https://www.youtube.com/user/NLMNIH/playlists"> <b> Link </b></a> </li> </td>  
150 |            </tr>
151 |            <tr>
152 |              <td> Bioinformatics Course at SLU by the SGBC </td>
153 |              <td> <li> <a href="https://sgbc.github.io/course/"> <b> Link </b></a> </li> </td>  
154 |            </tr>
155 |             <tr>
156 |              <td> NGSeminars by NGSchool </td>
157 |              <td> <li> <a href="https://www.youtube.com/watch?v=TLpjSmm-FEM&list=PLj4Zs4bjsI9rtj3_0LcbJ3t6LUVQbAtAI"> <b> Link </b></a> </li> 
158 |                   <li> <a href="https://github.com/NGSchoolEU/ngs22"> <b> Slides and Materials </b></a></li> </td> 
159 |            </tr>
160 |               <tr>
161 |              <td> Bioinformatics Core by Cancer Research UK Cambridge Institute </td>
162 |              <td> <li> <a href="https://www.cruk.cam.ac.uk/core-facilities/bioinformatics-core/training"> <b> Link </b></a> </li>  </td> 
163 |            </tr>   
164 |               <tr>
165 |              <td> Bioinformagician Channel </td>
166 |              <td> <li> <a href="https://www.youtube.com/@Bioinformagician"> <b> Link </b></a> </li>  </td> 
167 |              <tr>
168 |              <td> UCLA QCBio Collaboratory Channel </td>
169 |              <td> <li> <a href="https://www.youtube.com/@uclaqcbiocollaboratory3691/playlists"> <b> Link </b></a> </li>  </td> 
170 |            </tr>
171 |              <tr>
172 |               <td> Bioinformatics for Plant and Animal sciences </td>
173 |               <td> <li> <a href="https://www.youtube.com/playlist?list=PLhR2Go-lh6X5A5WbiO3SPHuoWbwpNznUl"> <b> Link </b> </a> </li></td>
174 |              </tr>
175 |               <td> Danny Arends Youtube Channel </td>
176 |               <td> <li> <a href="https://www.youtube.com/@DannyArends"> <b> Link </b> </a> </li></td>
177 |               <tr>
178 |               <td> Bioinformatics for Biologists 2021 </td>
179 |               <td> <li> <a href="https://biocorecrg.github.io/CRG_Bioinformatics_for_Biologists_2021/"> <b> Link </b> </a> </li></td> 
180 |               </tr>
181 |               <tr>
182 |               <td> video materials for the courses teached by Prof. Nathaniel Jue at California State University </td>
183 |               <td> <li> <a href="https://www.youtube.com/@nathanieljue2315/playlists"> <b> Link </b> </a> </li></td> 
184 |               </tr>
185 |               <tr>
186 |               <td> Modern Statistics for Modern Biology </td>
187 |               <td> <li> <a href="https://web.stanford.edu/class/bios221/book/"> <b> Link </b> </a> </li></td> 
188 |               </tr>
189 |               <tr>
190 |               <td> Statistics for heterogeneous biological data </td>
191 |               <td> <li> <a href="https://web.stanford.edu/class/bios221/"> <b> Link </b> </a> </li></td> 
192 |               </tr>
193 |               <tr>
194 |               <td> BIOINFORMATICS 1 by The University of Edinburg in UK </td>
195 |               <td> <li> <a href="https://www.inf.ed.ac.uk/teaching/courses/bio1/"> <b> Link </b> </a> </li></td> 
196 |               </tr>
197 |               <tr>
198 |               <td> BIOINFORMATICS 2 by The University of Edinburg in UK </td>
199 |               <td> <li> <a href="https://www.inf.ed.ac.uk/teaching/courses/bio2/"> <b> Link </b> </a> </li></td> 
200 |               </tr>
201 |               <tr>
202 |               <td> Biostatsquid: clear explanations and hands-on tutorials for analysing and interpreting biological data.  </td>
203 |               <td> <li> <a href="https://www.youtube.com/@biostatsquid/videos"> <b> Link </b> </a> </li></td> 
204 |               </tr>
205 |               <tr>
206 |               <td> Exploratory analysis of transcriptomics data in R.  </td>
207 |               <td> <li> <a href="https://tavareshugo.github.io/data-carpentry-rnaseq/"> <b> Link </b> </a> </li></td> 
208 |               </tr>
209 |               <tr>
210 |               <td> TileStats: courses in statistics and systems biology at the University of Skövde, Sweden by Prof. Andreas Tilevik.  </td>
211 |               <td> <li> <a href="https://www.youtube.com/@tilestats/playlists"> <b> Link </b> </a> </li></td> 
212 |               </tr>
213 |               <tr>
214 |               <td> A hands-on introduction to the computer-based analysis of genomic and biomolecular data from the Division of Biological Sciences, UCSD.  </td>
215 |               <td> <li> <a href="https://bioboot.github.io/bimm143_W20/"> <b> Link </b> </a> </li></td> 
216 |               </tr>
217 |               <tr>
218 |               <td> Danny Arends Bioinformatics YouTube channel </td>
219 |               <td> <li> <a href="https://dannyarends.nl/bioinformatik/"> <b> Lectures Links </b> </a> </li>
220 |               <li> <a href="https://www.youtube.com/@DannyArends/playlists"> <b> Videos Links </b> </a> </li></td>
221 |               </tr>
222 |               <tr>
223 |               <td> Erik Lindahl YouTube channel </td>
224 |               <td> <li> <a href="https://www.youtube.com/@eriklindahl/videos"> <b> Link </b> </a> </li></td>
225 |               </tr>
226 |               <tr>
227 |               <td> Gerald Quon YouTube channel </td>
228 |               <td> <li> <a href="https://www.youtube.com/@quonbio/videos"> <b> Link </b> </a> </li></td>
229 |               </tr>
230 |               <tr>
231 |               <td> Mike Saint-Antoine YouTube channel </td>
232 |               <td> <li> <a href="https://www.youtube.com/@MikeSaintAntoine/playlists"> <b> Link </b> </a> </li></td>
233 |               </tr>
234 |            </tr>
235 |   </table>
236 | 


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