Merge pull request #1 from BackofenLab/tutorial2

add additional tutorial materials

.gitignore

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+_build/

src/docs/tutorial/RBPs.md

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+
+# List of RBPs and number of available motifs
+
+The RBPs and motifs available in RBPBench are based on the curated list of motifs from [catRAPID omics](https://service.tartaglialab.com/page/catrapid_omics2_group) database. At present RBPBench hosts 605 motifs from 259 RBPs. The list of RBPs and number of motifs per RBP are given below:
+
+|  RBP | Number of motifs|
+|------|:---------------:|
+| A1CF | 2          |
+| ACIN1 | 2|
+| ACO1 | 1|
+| ADAR | 4|
+| AGGF1 | 2|
+| AGO1 | 1|
+| AGO2 | 2|
+| AKAP1 | 1|
+| AKAP8 | 1|
+| ANKHD1 | 1|
+| AUH | 2|
+| BCCIP | 1|
+| BOLL | 3|
+| BUD13 | 4|
+| CAPRIN1 | 1|
+| CBX7 | 1|
+| CDC40 | 2|
+| CELF1 | 1|
+| CELF2 | 2|
+| CELF4 | 1|
+| CELF5 | 1|
+| CELF6 | 1|
+| CNBP | 2|
+| CNOT4 | 1|
+| CPEB1 | 1|
+| CPEB2 | 1|
+| CPEB4 | 1|
+| CPSF6 | 1|
+| CPSF7 | 1|
+| CSTF2 | 2|
+| CSTF2T | 2|
+| DAZ3 | 4|
+| DAZAP1 | 4|
+| DDX3X | 2|
+| DDX6 | 1|
+| DDX19B | 1|
+| DDX24 | 2|
+| DDX54 | 2|
+| DDX55 | 6|
+| DDX58 | 1|
+| DDX59 | 1|
+| DGCR8 | 1|
+| DKC1 | 3|
+| EFTUD2 | 1|
+| EIF3D | 5|
+| EIF4A3 | 3|
+| EIF4B | 1|
+| EIF4G2 | 4|
+| ELAVL1 | 4|
+| ELAVL2 | 4|
+| ELAVL3 | 3|
+| ELAVL4 | 3|
+| ENOX1 | 1|
+| ERI1 | 1|
+| ESRP1 | 3|
+| ESRP2 | 1|
+| EWSR1 | 2|
+| FAM120A | 3|
+| FASTKD2 | 3|
+| FBL | 1|
+| FIP1L1 | 2|
+| FMR1 | 5|
+| FTO | 2|
+| FUBP1 | 3|
+| FUBP3 | 2|
+| FUS | 2|
+| FXR1 | 2|
+| FXR2 | 5|
+| G3BP1 | 2|
+| G3BP2 | 1|
+| GNL3 | 2|
+| GPKOW | 2|
+| GRSF1 | 2|
+| GRWD1 | 2|
+| GTF2F1 | 1|
+| HLTF | 1|
+| HNRNPA0 | 2|
+| HNRNPA1 | 7|
+| HNRNPA1L2 | 1|
+| HNRNPA2B1 | 4|
+| HNRNPA3 | 1|
+| HNRNPAB | 3|
+| HNRNPC | 2|
+| HNRNPCL1 | 1|
+| HNRNPD | 3|
+| HNRNPDL | 3|
+| HNRNPF | 1|
+| HNRNPH1 | 1|
+| HNRNPH2 | 1|
+| HNRNPK | 2|
+| HNRNPL | 5|
+| HNRNPLL | 2|
+| HNRNPM | 5|
+| HNRNPU | 6|
+| HNRNPUL1 | 4|
+| IFIH1 | 1|
+| IGF2BP1 | 4|
+| IGF2BP2 | 2|
+| IGF2BP3 | 1|
+| IGHMBP2 | 1|
+| ILF2 | 2|
+| ILF3 | 3|
+| KHDRBS1 | 2|
+| KHDRBS2 | 1|
+| KHDRBS3 | 2|
+| KHSRP | 5|
+| LARP4 | 3|
+| LARP4B | 1|
+| LIN28A | 1|
+| LIN28B | 1|
+| LSM11 | 4|
+| MATR3 | 1|
+| MBNL1 | 5|
+| METAP2 | 1|
+| MSI1 | 4|
+| MSI2 | 1|
+| MTPAP | 2|
+| NCBP2 | 3|
+| NELFE | 2|
+| NKRF | 3|
+| NOL12 | 2|
+| NONO | 2|
+| NOP56 | 1|
+| NOP58 | 1|
+| NOVA1 | 1|
+| NOVA2 | 4|
+| NPM1 | 2|
+| NSUN2 | 2|
+| NUMA1 | 1|
+| NUP42 | 2|
+| NXF1 | 1|
+| OAS1 | 1|
+| OBI1 | 1|
+| PABPC1 | 3|
+| PABPC3 | 1|
+| PABPC4 | 1|
+| PABPC5 | 1|
+| PABPN1 | 1|
+| PABPN1L | 1|
+| PARP1 | 2|
+| PCBP1 | 7|
+| PCBP2 | 9|
+| PCBP4 | 2|
+| PPIE | 2|
+| PPIG | 2|
+| PPIL4 | 5|
+| PPRC1 | 1|
+| PRPF8 | 3|
+| PRR3 | 2|
+| PTBP1 | 5|
+| PTBP2 | 1|
+| PTBP3 | 1|
+| PUF60 | 1|
+| PUM1 | 3|
+| PUM2 | 5|
+| QKI | 8|
+| RALY | 1|
+| RALYL | 1|
+| RANGAP1 | 1|
+| RBFOX1 | 4|
+| RBFOX2 | 2|
+| RBFOX3 | 1|
+| RBM3 | 1|
+| RBM4 | 2|
+| RBM4B | 3|
+| RBM5 | 3|
+| RBM6 | 1|
+| RBM8A | 1|
+| RBM10 | 2|
+| RBM14 | 1|
+| RBM15 | 1|
+| RBM15B | 2|
+| RBM22 | 7|
+| RBM23 | 2|
+| RBM24 | 1|
+| RBM25 | 4|
+| RBM28 | 1|
+| RBM39 | 1|
+| RBM41 | 1|
+| RBM42 | 1|
+| RBM45 | 5|
+| RBM46 | 1|
+| RBM47 | 1|
+| RBMS1 | 1|
+| RBMS2 | 1|
+| RBMS3 | 5|
+| RBMX | 2|
+| RBMY1A1 | 1|
+| RC3H1 | 2|
+| TROVE2 | 7|
+| RPS5 | 2|
+| SAFB2 | 2|
+| SAMD4A | 1|
+| SART3 | 1|
+| SF1 | 2|
+| SF3A3 | 4|
+| SF3B4 | 2|
+| SFPQ | 6|
+| SLTM | 1|
+| SMNDC1 | 2|
+| SND1 | 5|
+| SNRNP70 | 1|
+| SNRPA | 3|
+| SNRPB2 | 1|
+| SOX2 | 1|
+| SRP14 | 1|
+| SRP68 | 1|
+| SRRM4 | 2|
+| SRSF1 | 11|
+| SRSF2 | 8|
+| SRSF3 | 4|
+| SRSF4 | 2|
+| SRSF5 | 5|
+| SRSF6 | 4|
+| SRSF7 | 10|
+| SRSF8 | 2|
+| SRSF9 | 1|
+| SRSF10 | 5|
+| SRSF11 | 2|
+| SSB | 1|
+| SUB1 | 2|
+| SUGP2 | 2|
+| SUPV3L1 | 2|
+| SYNCRIP | 1|
+| TAF15 | 5|
+| TARBP2 | 3|
+| TARDBP | 3|
+| TBRG4 | 2|
+| TIA1 | 1|
+| TIAL1 | 2|
+| TNRC6A | 2|
+| TRA2A | 5|
+| TRA2B | 2|
+| TRNAU1AP | 2|
+| TUT1 | 2|
+| U2AF1 | 4|
+| U2AF2 | 3|
+| UCHL5 | 3|
+| UNK | 3|
+| UPF1 | 1|
+| WDR33 | 1|
+| XPO5 | 3|
+| XRCC6 | 4|
+| XRN2 | 3|
+| YBX1 | 3|
+| YBX2 | 1|
+| YBX3 | 1|
+| YTHDC1 | 1|
+| YWHAG | 1|
+| ZC3H10 | 1|
+| ZCRB1 | 1|
+| ZFP36 | 2|
+| ZFP36L2 | 2|
+| ZNF184 | 1|
+| ZNF326 | 3|
+| ZNF622 | 3|
+| ZNF638 | 1|
+| ZRANB2 | 4|
+| SLBP | 1 |

src/docs/tutorial/intro.md

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+# RBPBench user interface introduction
+
+RBPBench is intended to be primarily used as a tool within Galaxy.
+
+## Introduction to Galaxy
+
+If you are not familiar with the Galaxy ecosystem, please follow the  tutorials below and familiarize yourself with the Galaxy user interface and tools.
+
+- [A gentle introduction to the Galaxy user interface](https://usegalaxy.eu/tours/core.galaxy_ui)
+- [Galaxy history introduction](https://usegalaxy.eu/tours/core.history)
+- [Using Galaxy and Managing your Data](https://training.galaxyproject.org/training-material/topics/galaxy-interface/)
+- [Additional Galaxy training materials](https://training.galaxyproject.org/)
+- [Additional Galaxy interactive tours](https://usegalaxy.eu/tours)
+
+## Introduction to RBPBench user interface
+
+![RBPBench user interface](../../assets/images/rbpbench_ui_no_history.png)
+
+Figure above shows RBPBench user interface. Here users can select the progam mode, upload genomic regions of interest (ROI) as BED formatted files and either upload a custom reference genome sequence or use one of the built-in reference sequences.
+
+### Program modes
+
+![RBPBench run modes](../../assets/images/rbpbench_program_modes.png)
+
+Figure above shows various run modes available in RBPBench. A brief description of these modes are given below:
+
+#### Search RBP binding motifs
+
+There are **three** search modes in RBPBench
+
+1. **Search RBP binding motifs in genomic regions**
+
+    Given a single set of binding regions (in BED format), search for motifs from multiple RBPs.
+
+2. **Search RBP binding motifs in genomic regions (multiple inputs)**
+
+    Given two or more sets of binding regions (in BED format), search for motifs from multiple RBPs.
+
+3. **Search RBP binding motifs in genomic regions (data collection input)**
+
+    This search mode is identical to the previous mode to use multiple binding regions. The difference being that an additional data description table with such meta information such as RBP, method ID, data ID and file name to be uploaded along with the input data.
+    Example table format:
+
+    | RBP | method          | data ID     | file name       |
+    |-----|-----------------|-------------|-----------------|
+    | PUM1| analysis_method1| PUM1_method1| PUM1_method1.bed|
+    | PUM1| analysis_method2| PUM1_method2| PUM1_method2.bed|
+    | PUM2| analysis_method1| PUM2_method1| PUM2_method1.bed|
+    | PUM2| analysis_method2| PUM2_method2| PUM2_method2.bed|
+
+#### Compare different search results
+
+This mode is used to compare different motif search results (produced by any of the three motif search modes described above)
+
+#### Plot nucleotide distribution at genomic positions
+
+Given a set of genomic regions, center the regions around a user specified nucleotide position,  extend upstream and downstream of all regions by a given length and plot nucleotide distribution.

src/index.md

@@ -1,28 +1,36 @@
 # RBPBench
 
-RBPBench is multi-function tool to evaluate CLIP-seq and other genomic region data 
-using a comprehensive collection of known RBP binding motifs. RBPBench can be used 
-for a variety of purposes, from RBP motif search (database or user-supplied RBPs) 
-in genomic regions, over motif co-occurrence analysis, to benchmarking CLIP-seq peak 
+[RBPBench](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/rnateam/rbpbench/rbpbench/0.7+galaxy0) is multi-function tool to evaluate CLIP-seq and other genomic region data
+using a comprehensive collection of known RBP binding motifs. RBPBench can be used
+for a variety of purposes, from RBP motif search (database or user-supplied RBPs)
+in genomic regions, over motif co-occurrence analysis, to benchmarking CLIP-seq peak
 caller methods as well as comparisons across cell types and CLIP-seq protocols.
 
-## Links
+## [RBPBench Webserver on Galaxy](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/rnateam/rbpbench/rbpbench/0.7+galaxy0)
 
-RBPBench [Webserver on Galaxy](https://usegalaxy.eu/)
-
-RBPBench [Webserver Tutorial](https://usegalaxy.eu/)
-
-RBPBench [GitHub repository](https://github.com/michauhl/RBPBench)
+## RBPBench Galaxy Tutorials
 
+- [Basic Galaxy introduction and RBPBench user interface](docs/tutorial/intro.md)
 
+## RBPBench results
 
 ![RBPBench example visualizations](assets/images/rbpbench_visualization_examples.png)
 <span style="font-size: 90%;">
-**Figure**: Some example visualizations produced by RBPBench. 
-**a**: RBP binding motif co-occurrence heat map. 
-**b**: What RBP binding motif combinations appear in the data. 
-**c**: Motif distances in the data relative to an RBP of interest. 
-**d**: To which region types RBPs preferentially bind to. 
-**e**: Comparing CLIP-seq peak calling methods. 
+**Figure**: Some example visualizations produced by RBPBench.
+**a**: RBP binding motif co-occurrence heat map.
+**b**: What RBP binding motif combinations appear in the data.
+**c**: Motif distances in the data relative to an RBP of interest.
+**d**: To which region types RBPs preferentially bind to.
+**e**: Comparing CLIP-seq peak calling methods.
 **f**: Comparing experimental conditions.
 </span>
+
+## Additional Links
+
+RBPBench [GitHub repository](https://github.com/michauhl/RBPBench)
+
+RBPBench [Bioconda package](https://bioconda.github.io/recipes/rbpbench/README.html)
+
+## RBP motif data
+
+List of [RBPs and number of available motifs per RBP](docs/tutorial/RBPs.md)