ARMOR | weight Snakemake workflow | Genomics library

 by   csoneson R Version: v1.0 License: MIT

kandi X-RAY | ARMOR Summary

kandi X-RAY | ARMOR Summary

ARMOR is a R library typically used in Artificial Intelligence, Genomics applications. ARMOR has no bugs, it has no vulnerabilities, it has a Permissive License and it has low support. You can download it from GitHub.

ARMOR (Automated Reproducible MOdular RNA-seq) is a Snakemake workflow, aimed at performing a typical RNA-seq workflow in a reproducible, automated, and partially contained manner. It is implemented such that alternative or similar analysis can be added or removed. ARMOR consists of a Snakefile, a conda environment file (envs/environment.yaml) a configuration file (config.yaml) and a set of R scripts, to perform quality control, preprocessing and differential expression analysis of RNA-seq data. The output can be combined with the iSEE R package to generate a shiny application for browsing and sharing the results. By default, the pipeline performs all the steps shown in the diagram below. However, you can turn off any combination of the light-colored steps (e.g STAR alignment or DRIMSeq analysis) in the config.yaml file. Advanced use: If you prefer other software to run one of the outlined steps (e.g. DESeq2 over edgeR, or kallisto over Salmon), you can use the software of your preference provided you have your own script(s), and change some lines within the Snakefile. If you think your "custom rule" might be of use to a broader audience, let us know by opening an issue.
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            kandi-support Support

              ARMOR has a low active ecosystem.
              It has 116 star(s) with 28 fork(s). There are 13 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 0 open issues and 53 have been closed. On average issues are closed in 21 days. There are no pull requests.
              It has a neutral sentiment in the developer community.
              The latest version of ARMOR is v1.0

            kandi-Quality Quality

              ARMOR has no bugs reported.

            kandi-Security Security

              ARMOR has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

            kandi-License License

              ARMOR is licensed under the MIT License. This license is Permissive.
              Permissive licenses have the least restrictions, and you can use them in most projects.

            kandi-Reuse Reuse

              ARMOR releases are available to install and integrate.
              Installation instructions are not available. Examples and code snippets are available.

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            Currently covering the most popular Java, JavaScript and Python libraries. See a Sample of ARMOR
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            ARMOR Key Features

            No Key Features are available at this moment for ARMOR.

            ARMOR Examples and Code Snippets

            Installs the specified armor
            javadot img1Lines of Code : 3dot img1no licencesLicense : No License
            copy iconCopy
            void equipArmor(Armor armor){
                    this.armor = armor;
                }  

            Community Discussions

            QUESTION

            How calculate changing slider values with a maximum value for all?
            Asked 2021-Jun-14 at 16:31

            I need to create a slider for a game that you can set skills to each player,

            The rules are :

            1. Each skill starts at 0.
            2. The skills cannot total more than 100 points at any time.
            3. It should always be possible to assign any 0-100 value to a given skill. Given rule (2), if this gets us over 100 total points, the excess automatically, immediately, removed from the other skills, according to their current values.
            4. It's not required to use all 100 points (or any).
            5. A skill's value is always an integer.

            For example :

            • We start with:
              Stamina: 0 | Speed: 0 | Armor: 0 | Strength: 0 | Remaining: 100

            • The player adds 50 Speed.
              Stamina: 0 | Speed: 50 | Armor: 0 | Strength: 0 | Remaining: 50

            • The player adds 25 Armor.
              Stamina: 0 | Speed: 50 | Armor: 25 | Strength: 0 | Remaining: 25 - 115

            • The player now adds 40 Stamina. The excess is automatically reduced from the other skills, weighted by their current values.
              Stamina: 40 | Speed: 40 | Armor: 20 | Strength: 0 | Remaining: 0

            • The player then reduces Speed to 10.
              Stamina: 40 | Speed: 30 | Armor: 20 | Strength: 0 | Remaining: 10

            • Finally, the player sets Strength to 100.
              Stamina: 0 | Speed: 0 | Armor: 0 | Strength: 100 | Remaining: 0

            To do so i've created a function the receives 3 arguments :

            1. An array of values of the slider

            let arrToCalc = [14,24,55,0]

            1. The index number of the skill (0 for Stamina, 1 for Speed ...etc)

            let newValueIndex = 2

            1. New value for base the calculation on

            let newVal = 64.

            Im not sure my calculations are accurate so i'm getting partial good results.

            when set to

            ...

            ANSWER

            Answered 2021-Jun-13 at 06:59

            After calculating the total score, reduce that from 100, and store it in the variable (here extra), then run a while loop utill that value becomes 0.

            In the below snippet, I am running a loop and in each iteration reducing the value by 10. You can change the reduction logic as per the requirement.

            Source https://stackoverflow.com/questions/67955543

            QUESTION

            Python variable is being updated on each loop even though I initialized it outside of the loop
            Asked 2021-Jun-11 at 01:52

            Working on a little Fallout minigame in python...

            I have a function called level_up that allows player to distribute skill points.

            Player's current stats are stored as attributes of the player class.

            I created a variable inside the level_up function that copies the player's current stats to compare against while the leveling loop is running. I did this so that the player cannot edit the stat value to be less than what it was when the level up occurred.

            I initialized this variable outside of the main loop of the function in order to have it be constant, but as the player makes edits to their stats, this variable (original values) seems to be updated with the new values, instead of staying at what the values were when the level up occurred.

            Example (Billy's Small Guns skill is 15 when he levels up. original_values should store that 15 was the original value. Billy adds 5 points to Small Guns, making it 20. He decides he wants to go back to 15. Should work since the original value was 15, but original_values now has Small Guns at 20, so this change can't occur).

            I thought initializing original_values outside the loop is what I would need to do. Does this have something to do with the fact that I'm updating class attributes?

            Can anyone tell me what I am doing wrong? Thank you.

            The Function

            ...

            ANSWER

            Answered 2021-Jun-11 at 01:52

            original_values = self.combat_skills does not make a copy. It's just another reference to the same object - changes made via one reference will be seen no matter which reference you use to access them because they're all the same object.

            If you want to make a distinct copy use the copy method of the dict to make a copy. e.g. original_values = self.combat_skills.copy()

            Source https://stackoverflow.com/questions/67930307

            QUESTION

            Why does IntelliJ generate different import statements for .spec files?
            Asked 2021-Jun-03 at 15:03

            I wonder why the IntelliJ Add import statement works differently when used in a spec file:

            The setup is very simple.
            In the project tsconfig.base.ts file we specify a path:

            ...

            ANSWER

            Answered 2021-Jun-03 at 15:03

            With Use path mappings from tsconfig.json set to Always, the IDE tries to use the mappings any time the import is added. But, as "@idea-import-spec/data" is mapped to libs/data/src/index.ts that, in turn, re-exports everything from lib/data.ts, adding a mapped import to data.ts would result in a circular dependency - that's why a relative path is used. But data.spec.ts is not re-exported in barrel, so using a path mappings there looks safe

            Source https://stackoverflow.com/questions/67821309

            QUESTION

            How can I assign all objects in a vector in one line? OOP C++
            Asked 2021-May-30 at 13:30

            There is class called Player and has std::vectorstd::shared_ptr library vector. In the int main part, I created objects called Soldier, Pegasus, Guard. I wanna pass this object into a vector in one line. How can I do that? Basically, I wanna create a player1 deck of card vector and pass the objects into that vector.

            ...

            ANSWER

            Answered 2021-May-30 at 13:30
            #include
            
            class Card{
            };
            class Creature : public Card
            {
            private:
                std::string name;
                int a, b, c;
                bool d, e;
                char f;
                
            public:
                Creature(std::string name, int a, int b, int c, bool d, bool e, char f) : Card(), name(name), a(a), b(b), c(c), d(d), e(e), f(f) {};
            };
            
            class Player{
            private:
                using Cards = std::vector>;
                Cards library;
            public:
                Player(Cards cards): library(cards){}
            };
            
            int main(){
            
            std::shared_ptr Soldier = std::make_shared("Soldier", 0, 1, 1, false, false, 'W');
            std::shared_ptr Guard = std::make_shared("Guard", 2, 2, 5, false, false,'W');
            std::shared_ptr ArmoredPegasus = std::make_shared("Armored Pegasus", 1, 1, 2, false, false,'W');
            
            Player player1({Soldier, ArmoredPegasus, Guard});
            }
            

            Source https://stackoverflow.com/questions/67761517

            QUESTION

            Can't deserialize JSON into an object with nested list
            Asked 2021-May-26 at 14:30

            Apologies for asking a fairly common question, I have been looking all over and can't find a solution that fixes my problem.

            I am using Firesharp, and trying to deserialize a Json object that Firebase returns into a class with a nested list.

            ...

            ANSWER

            Answered 2021-May-26 at 14:30

            This in no way a complete answer. I assume you don't want to map/create classes for each "sub class", e.g. Barbarian, Wizard etc. You could perhaps use JsonConverter. The example only handles the first "anonymous" range of objects. Maybe you'll find some of this useful.

            Source https://stackoverflow.com/questions/67702360

            QUESTION

            How can I remove a level in a JSON file?
            Asked 2021-May-25 at 18:11

            I have this JSON in my js script that goes on for another 150 elements :

            ...

            ANSWER

            Answered 2021-May-25 at 18:11
            const champs = champList.map(obj => {
                const champ = obj.data
                return Object.values(champ)
            })
            

            Source https://stackoverflow.com/questions/67693022

            QUESTION

            APCSP create task issue - Method ends program after being called
            Asked 2021-May-21 at 16:19

            I am creating a short RPG game for my AP CSP project and for some reason when I call the method Element in line 310-313, it just ends the rest of the code in Main (which is all the remaining code in the program). The user is required to press x to continue the game but it skips all of that and auto-fills the user-inputs correctly. Put it short, once you select your element in the code, the program finishes the game by itself, which is not supposed to happen since the user needs to have its input to continue the dialogue.

            Aforementioned, the intended output of this code is to complete the dialogue with the user input and user information only. Please help as this is due soon!

            ...

            ANSWER

            Answered 2021-May-11 at 07:49

            It looks like you stopped following the pattern that you applied in the beginning. As you'll see, prior to line 310, you have used

            Source https://stackoverflow.com/questions/67479847

            QUESTION

            Cloud Armor logs aren't very clear when rule is set as "Preview only"
            Asked 2021-May-21 at 08:27

            I'm deploying WAF with Cloud Armor and I realized that the rules can be created in a "Preview only" mode and that there are Cloud Armor entries in Cloud Logging.

            The problem is that when I create a "Preview only" rule and that rule is matched by some request, I cannot differentiate, in the logs, the requests that matched some specific rule and/or the normal, ordinary requests. They look all pretty much the same.

            Are there any logging attributes that only exist (or have specific values) when the request match a specific rule in these cases? Because the only way I found to explicitly check the rules matched by some request is unchecking the "Preview only" flag, and it is not nice for production when testing.

            ...

            ANSWER

            Answered 2021-May-21 at 01:27

            When you have rules configured in Cloud Armor set to "Preview", Cloud Logging will record what the rule would have done if enabled.

            This Cloud Logging filter will show you entries that were denied by Cloud Armor:

            Source https://stackoverflow.com/questions/67629608

            QUESTION

            How can I increase an int value from a method in Java
            Asked 2021-May-14 at 18:22

            Using the example below. I want to see how to increase a number by calling a method occasionally. In this example, a hero would get armor, and his armor(totalArmor) would increase each time new armor was picked up. I tried 2 outputs one that would be 0 and the other that I would hope would do 2. Thanks.

            ...

            ANSWER

            Answered 2021-May-14 at 18:17

            QUESTION

            Get Values from a list in flutter
            Asked 2021-May-11 at 20:13

            I'm building a UI on flutter using some dummy data. I have modelled a class named movies

            ...

            ANSWER

            Answered 2021-May-11 at 20:13
            1. First of all, you should add "require" in your class. Otherwise dart will give you a similar error like the next one:

            line 51 • The parameter 'movieName' can't have a value of 'null' because of its type, but the implicit default value is 'null'. (view docs) Try adding either an explicit non-'null' default value or the 'required' modifier.

            1. Import the class and the example information where you need it.

              import 'package:exampleapp/movie_list_sample_information.dart;

              import 'package:exampleapp/movies.dart;

            2. Use the variable to get the information

              movieLists[0].movieName // gets the first movie of your list

            The next dartpad uses your code as example: https://dartpad.dev/95d67aa68267296ac3fd8a56405b2880?null_safety=true

            Press "Run" button and you should see the name of the first movie in "Console"

            EDIT:

            To read the list in dynamically in flutter you can use ListView.builder

            Source https://stackoverflow.com/questions/67493451

            Community Discussions, Code Snippets contain sources that include Stack Exchange Network

            Vulnerabilities

            No vulnerabilities reported

            Install ARMOR

            You can download it from GitHub.

            Support

            For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .
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            https://github.com/csoneson/ARMOR.git

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            gh repo clone csoneson/ARMOR

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            git@github.com:csoneson/ARMOR.git

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