diff --git a/Implementation.md b/Implementation.md index b743693..43ff100 100644 --- a/Implementation.md +++ b/Implementation.md @@ -24,7 +24,7 @@ ---- # **Introduction** -The **RiboMiner** is a python package used for downstream analysis of ribosome profiling data. This package has four function parts: +The **[RiboMiner](https://github.com/xryanglab/RiboMiner)** is a python toolset for mining multi-dimensional features of the translatome with ribosome profiling data. This package has four function parts: + **Quality Control (QC)**: Quality control for ribosome profiling data, containing periodicity checking, reads distribution among different reading frames,length distribution of ribosome footprints and DNA contaminations. @@ -32,7 +32,7 @@ The **RiboMiner** is a python package used for downstream analysis of ribosome p + **Feature Analysis (FA)**: Feature analysis among different gene sets identified in MA step to explain the possible ribosome stalling. + **Enrichment Analysis (EA)**: Enrichment analysis to find possible co-translation events. -In this file, we will show you how to use our **RiboMiner** based on some published datasets. +In this file, we will show you how to use our **[RiboMiner](https://github.com/xryanglab/RiboMiner)** based on some published datasets. # **Data preparation (DP)** @@ -424,38 +424,39 @@ EnrichmentAnalysisForSingleTrans -i all_codon_ratio.txt.txt -s ARC1 -o ARC1 -c < ``` ![EA.png-284.3kB][31] -**Figure 6: The results of Enrichment Analysis**. **A.** Engagement of nascent ARC1 (top), GUS1 (bottom) by C-terminally tagged MetRS. **B.** Engagement of nascent ARC1 (top), MES1 (bottom) by C-terminally tagged GluRS. - - - - [1]: http://static.zybuluo.com/sherking/fhl1830e4ymca16oezezn4eg/QC.png - [2]: http://static.zybuluo.com/sherking/fhl1830e4ymca16oezezn4eg/QC.png - [3]: http://static.zybuluo.com/sherking/fhl1830e4ymca16oezezn4eg/QC.png - [4]: http://static.zybuluo.com/sherking/fhl1830e4ymca16oezezn4eg/QC.png - [5]: http://static.zybuluo.com/sherking/fhl1830e4ymca16oezezn4eg/QC.png - [6]: http://static.zybuluo.com/sherking/fhl1830e4ymca16oezezn4eg/QC.png - [7]: http://static.zybuluo.com/sherking/fhl1830e4ymca16oezezn4eg/QC.png - [8]: http://static.zybuluo.com/sherking/2pi6e3rq2sr052lqbqxjs3so/MA.png - [9]: http://static.zybuluo.com/sherking/2pi6e3rq2sr052lqbqxjs3so/MA.png - [10]: http://static.zybuluo.com/sherking/2pi6e3rq2sr052lqbqxjs3so/MA.png - [11]: http://static.zybuluo.com/sherking/2pi6e3rq2sr052lqbqxjs3so/MA.png - [12]: http://static.zybuluo.com/sherking/2pi6e3rq2sr052lqbqxjs3so/MA.png - [13]: http://static.zybuluo.com/sherking/2pi6e3rq2sr052lqbqxjs3so/MA.png - [14]: http://static.zybuluo.com/sherking/l9cjetv127vexf8dc6pwth5q/AADensity.png - [15]: http://static.zybuluo.com/sherking/l9cjetv127vexf8dc6pwth5q/AADensity.png - [16]: http://static.zybuluo.com/sherking/l9cjetv127vexf8dc6pwth5q/AADensity.png - [17]: http://static.zybuluo.com/sherking/l9cjetv127vexf8dc6pwth5q/AADensity.png - [18]: http://static.zybuluo.com/sherking/l9cjetv127vexf8dc6pwth5q/AADensity.png - [19]: http://static.zybuluo.com/sherking/l9cjetv127vexf8dc6pwth5q/AADensity.png - [20]: http://static.zybuluo.com/sherking/l9cjetv127vexf8dc6pwth5q/AADensity.png - [21]: http://static.zybuluo.com/sherking/vpx5pimueh9w3d7gr2o5hppw/triAADensity.png - [22]: http://static.zybuluo.com/sherking/vpx5pimueh9w3d7gr2o5hppw/triAADensity.png - [23]: http://static.zybuluo.com/sherking/vpx5pimueh9w3d7gr2o5hppw/triAADensity.png - [24]: http://static.zybuluo.com/sherking/vpx5pimueh9w3d7gr2o5hppw/triAADensity.png - [25]: http://static.zybuluo.com/sherking/1j4txn5zno1pex79c5ja1bqx/CAItAI.png - [26]: http://static.zybuluo.com/sherking/1j4txn5zno1pex79c5ja1bqx/CAItAI.png - [27]: http://static.zybuluo.com/sherking/1j4txn5zno1pex79c5ja1bqx/CAItAI.png - [28]: http://static.zybuluo.com/sherking/1j4txn5zno1pex79c5ja1bqx/CAItAI.png - [29]: http://static.zybuluo.com/sherking/vpx5pimueh9w3d7gr2o5hppw/triAADensity.png - [30]: http://static.zybuluo.com/sherking/1j4txn5zno1pex79c5ja1bqx/CAItAI.png - [31]: http://static.zybuluo.com/sherking/jjy5h149wmn9cudfbpijffwy/EA.png \ No newline at end of file +**Figure 6: The results of Enrichment Analysis**. **A.** Engagement of nascent ARC1 (top), GUS1 (bottom) by C-terminally tagged MetRS. **B.** Engagement of nascent ARC1 (top), MES1 (bottom) by C-terminally tagged GluRS. The red dotted lines represent twofold threshold. + + + + + [1]: http://static.zybuluo.com/sherking/4wuu4omw1r3edhnhxoalot9q/QC2.png + [2]: http://static.zybuluo.com/sherking/4wuu4omw1r3edhnhxoalot9q/QC2.png + [3]: http://static.zybuluo.com/sherking/4wuu4omw1r3edhnhxoalot9q/QC2.png + [4]: http://static.zybuluo.com/sherking/4wuu4omw1r3edhnhxoalot9q/QC2.png + [5]: http://static.zybuluo.com/sherking/4wuu4omw1r3edhnhxoalot9q/QC2.png + [6]: http://static.zybuluo.com/sherking/4wuu4omw1r3edhnhxoalot9q/QC2.png + [7]: http://static.zybuluo.com/sherking/4wuu4omw1r3edhnhxoalot9q/QC2.png + [8]: http://static.zybuluo.com/sherking/v59lhdcvwk57fya119a4r3rq/MA.png + [9]: http://static.zybuluo.com/sherking/v59lhdcvwk57fya119a4r3rq/MA.png + [10]: http://static.zybuluo.com/sherking/v59lhdcvwk57fya119a4r3rq/MA.png + [11]: http://static.zybuluo.com/sherking/v59lhdcvwk57fya119a4r3rq/MA.png + [12]: http://static.zybuluo.com/sherking/v59lhdcvwk57fya119a4r3rq/MA.png + [13]: http://static.zybuluo.com/sherking/v59lhdcvwk57fya119a4r3rq/MA.png + [14]: http://static.zybuluo.com/sherking/rl0wsq9zbrgnjg5f8alz00p5/AADensity.png + [15]: http://static.zybuluo.com/sherking/rl0wsq9zbrgnjg5f8alz00p5/AADensity.png + [16]: http://static.zybuluo.com/sherking/rl0wsq9zbrgnjg5f8alz00p5/AADensity.png + [17]: http://static.zybuluo.com/sherking/rl0wsq9zbrgnjg5f8alz00p5/AADensity.png + [18]: http://static.zybuluo.com/sherking/rl0wsq9zbrgnjg5f8alz00p5/AADensity.png + [19]: http://static.zybuluo.com/sherking/rl0wsq9zbrgnjg5f8alz00p5/AADensity.png + [20]: http://static.zybuluo.com/sherking/rl0wsq9zbrgnjg5f8alz00p5/AADensity.png + [21]: http://static.zybuluo.com/sherking/r1oq3on8woelch6m307te3o4/triAADensity.png + [22]: http://static.zybuluo.com/sherking/r1oq3on8woelch6m307te3o4/triAADensity.png + [23]: http://static.zybuluo.com/sherking/r1oq3on8woelch6m307te3o4/triAADensity.png + [24]: http://static.zybuluo.com/sherking/r1oq3on8woelch6m307te3o4/triAADensity.png + [25]: http://static.zybuluo.com/sherking/r877xvlk0zyf0q6mfelxzbiv/CAItAI.png + [26]: http://static.zybuluo.com/sherking/r877xvlk0zyf0q6mfelxzbiv/CAItAI.png + [27]: http://static.zybuluo.com/sherking/r877xvlk0zyf0q6mfelxzbiv/CAItAI.png + [28]: http://static.zybuluo.com/sherking/r877xvlk0zyf0q6mfelxzbiv/CAItAI.png + [29]: http://static.zybuluo.com/sherking/r1oq3on8woelch6m307te3o4/triAADensity.png + [30]: http://static.zybuluo.com/sherking/r877xvlk0zyf0q6mfelxzbiv/CAItAI.png + [31]: http://static.zybuluo.com/sherking/ae5qqlvl8x8nfr157vy7gpgu/EA.png diff --git a/README.md b/README.md index bb9d68a..ecfa178 100644 --- a/README.md +++ b/README.md @@ -17,7 +17,7 @@ --- # **Introduction** -The **RiboMiner** is a python package used for downstream analysis of ribosome profiling data. This package has four function parts: +The **RiboMiner** is a python toolset for mining multi-dimensional features of the translatome with ribosome profiling data. This package has four function parts: + **Quality Control (QC)**: Quality control for ribosome profiling data, containing periodicity checking, reads distribution among different reading frames,length distribution of ribosome footprints and DNA contaminations. @@ -44,7 +44,7 @@ The **RiboMiner** is a python package used for downstream analysis of ribosome p # **Installation** -**[RiboMiner](https://github.com/sherkinglee/RiboMiner)** can be installed like any other Python packages. Here are some popular ways: +**[RiboMiner](https://github.com/xryanglab/RiboMiner)** can be installed like any other Python packages. Here are some popular ways: + Install via pypi: ``` @@ -53,7 +53,7 @@ pip install RiboMiner + Install from source: ``` -git clone https://github.com/sherkinglee/RiboMiner.git +git clone https://github.com/xryanglab/RiboMiner.git cd RiboMiner python setup.py install ``` @@ -64,7 +64,7 @@ python setup.py install ## **Data preparation (DP)** -The analysis based on this package need some transcript sequences and annotation file. Before starting the analysis, we need to prepare those files ahead of time. However, the basic annotation file such genome FASTA file, GTF file for annotation which may be used for mapping need to be downloaded by user themselves. +The analysis based on this package need some transcript sequences and annotation file. Before starting the analysis, we need to prepare those files ahead of time. However, the basic annotation file such genome FASTA file, GTF file for annotation which may be used for mapping need to be downloaded by user themselves from [ensemble](http://www.ensembl.org/info/data/ftp/index.html). + **Prepare sequences and annotaiton files on transcriptome level.** @@ -469,4 +469,4 @@ EnrichmentAnalysisForSingleTrans -i -s