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Final Project #10

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Final Project #10

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Commits on Jan 13, 2019

  1. Initial commit

    @caseywdunn
    caseywdunn committed Jan 13, 2019
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  2. pulled over text from data class 

    from https://github.com/Brown-BIOL2430-S04-Fall2015/finalproject/blob/master/README.md
    @caseywdunn
    caseywdunn committed Jan 13, 2019
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  3. customized

    @caseywdunn
    caseywdunn committed Jan 13, 2019
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Commits on Jan 31, 2019

  1. small additions

    @caseywdunn
    caseywdunn committed Jan 31, 2019
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Commits on Feb 14, 2019

  1. added git ignore

    @caseywdunn
    caseywdunn committed Feb 14, 2019
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  2. added files so far

    @jasminelmah
    jasminelmah committed Feb 14, 2019
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  3. added files so far

    @jasminelmah
    jasminelmah committed Feb 14, 2019
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  4. ok actually added files.

    @jasminelmah
    jasminelmah committed Feb 14, 2019
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  5. ok actually added files.

    @jasminelmah
    jasminelmah committed Feb 14, 2019
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  6. updated readme.

    @jasminelmah
    jasminelmah committed Feb 14, 2019
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  7. updated readme.

    @jasminelmah
    jasminelmah committed Feb 14, 2019
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  8. trying to get citations to work in md.

    @jasminelmah
    jasminelmah committed Feb 14, 2019
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  9. trying to get citations to work in md.

    @jasminelmah
    jasminelmah committed Feb 14, 2019
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  10. still trying to get citations to work.

    @jasminelmah
    jasminelmah committed Feb 14, 2019
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  11. still trying to get citations to work.

    @jasminelmah
    jasminelmah committed Feb 14, 2019
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  12. refs working

    @jasminelmah
    jasminelmah committed Feb 14, 2019
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  13. refs working

    @jasminelmah
    jasminelmah committed Feb 14, 2019
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Commits on Feb 15, 2019

  1. small changes to readme and neurogenes notebook.

    @jasminelmah
    jasminelmah committed Feb 15, 2019
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  2. small changes to readme and neurogenes notebook.

    @jasminelmah
    jasminelmah committed Feb 15, 2019
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  3. started synteny readings notes.

    @jasminelmah
    jasminelmah committed Feb 15, 2019
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  4. started synteny readings notes.

    @jasminelmah
    jasminelmah committed Feb 15, 2019
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  5. looking for scaffold N50s

    @jasminelmah
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  6. looking for scaffold N50s

    @jasminelmah
    jasminelmah committed Feb 15, 2019
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  7. found the rest of my scaffold N50s.

    @jasminelmah
    jasminelmah committed Feb 15, 2019
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  8. found the rest of my scaffold N50s.

    @jasminelmah
    jasminelmah committed Feb 15, 2019
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  9. deposited cteno and por genomes and gffs (no gff for Oscarella).

    @jasminelmah
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  10. deposited cteno and por genomes and gffs (no gff for Oscarella).

    @jasminelmah
    jasminelmah committed Feb 15, 2019
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  11. added genomes and gffs meta data. Tried to add actual genome/gff file… 

    …s but trouble with git lfs.
    @jasminelmah
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  12. added genomes and gffs meta data. Tried to add actual genome/gff file… 

    …s but trouble with git lfs.
    @jasminelmah
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  13. meta data inputted. found genomes and gff files but trouble with git … 

    …lfs.
    @jasminelmah
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  14. meta data inputted. found genomes and gff files but trouble with git … 

    …lfs.
    @jasminelmah
    jasminelmah committed Feb 15, 2019
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Commits on Feb 16, 2019

  1. little notes

    @jasminelmah
    jasminelmah committed Feb 16, 2019
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  2. little notes

    @jasminelmah
    jasminelmah committed Feb 16, 2019
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Commits on Feb 19, 2019

  1. added to Liu et al review notes.

    @jasminelmah
    jasminelmah committed Feb 19, 2019
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  2. added to Liu et al review notes.

    @jasminelmah
    jasminelmah committed Feb 19, 2019
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Commits on Feb 20, 2019

  1. Struggled with SynChro file types (no avail). Notes for Ramos' method.

    @jasminelmah
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  2. Struggled with SynChro file types (no avail). Notes for Ramos' method.

    @jasminelmah
    jasminelmah committed Feb 20, 2019
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  3. more notes, added papers.

    @jasminelmah
    jasminelmah committed Feb 20, 2019
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  4. more notes, added papers.

    @jasminelmah
    jasminelmah committed Feb 20, 2019
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  5. removed papers. they just take up memory.

    @jasminelmah
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  6. removed papers. they just take up memory.

    @jasminelmah
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Commits on Feb 21, 2019

  1. :S

    @jasminelmah
    jasminelmah committed Feb 21, 2019
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  2. :S

    @jasminelmah
    jasminelmah committed Feb 21, 2019
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Commits on Mar 2, 2019

  1. fasta of all genes from table that I could find on NCBI. Took a crazy… 

    … long time yeesh.:
    @jasminelmah
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  2. fasta of all genes from table that I could find on NCBI. Took a crazy… 

    … long time yeesh.:
    @jasminelmah
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Commits on Mar 3, 2019

  1. Added csv of original fasta seq names.

    @jasminelmah
    jasminelmah committed Mar 3, 2019
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  2. Added csv of original fasta seq names.

    @jasminelmah
    jasminelmah committed Mar 3, 2019
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  3. cleaned up files

    @jasminelmah
    jasminelmah committed Mar 3, 2019
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  4. cleaned up files

    @jasminelmah
    jasminelmah committed Mar 3, 2019
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  5. setting up Synima still.

    @jasminelmah
    jasminelmah committed Mar 3, 2019
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  6. setting up Synima still.

    @jasminelmah
    jasminelmah committed Mar 3, 2019
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Commits on Mar 4, 2019

  1. quick save

    @jasminelmah
    jasminelmah committed Mar 4, 2019
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  2. quick save

    @jasminelmah
    jasminelmah committed Mar 4, 2019
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  3. wrote tiny R script for scaffold length histograms.

    @jasminelmah
    jasminelmah committed Mar 4, 2019
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  4. wrote tiny R script for scaffold length histograms.

    @jasminelmah
    jasminelmah committed Mar 4, 2019
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  5. renamed fasta

    @jasminelmah
    jasminelmah committed Mar 4, 2019
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  6. renamed fasta

    @jasminelmah
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  7. tweaking histogram code but looping isn't working. sucky.

    @jasminelmah
    jasminelmah committed Mar 4, 2019
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  8. tweaking histogram code but looping isn't working. sucky.

    @jasminelmah
    jasminelmah committed Mar 4, 2019
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  9. calling it a night

    @jasminelmah
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  10. calling it a night

    @jasminelmah
    jasminelmah committed Mar 4, 2019
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Commits on Mar 11, 2019

  1. added Methods

    @jasminelmah
    jasminelmah committed Mar 11, 2019
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  2. added Methods

    @jasminelmah
    jasminelmah committed Mar 11, 2019
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Commits on Mar 12, 2019

  1. changed readme to reflect new project goals (trimmed w/ Casey's help)

    @jasminelmah
    jasminelmah committed Mar 12, 2019
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  2. changed readme to reflect new project goals (trimmed w/ Casey's help)

    @jasminelmah
    jasminelmah committed Mar 12, 2019
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Commits on Mar 14, 2019

  1. wrote R script to check distribution of no. genes per contig. it's ho… 

    …rrible! sacre bleu
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  2. wrote R script to check distribution of no. genes per contig. it's ho… 

    …rrible! sacre bleu
    @jasminelmah
    jasminelmah committed Mar 14, 2019
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  3. file cleanup

    @jasminelmah
    jasminelmah committed Mar 14, 2019
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  4. file cleanup

    @jasminelmah
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Commits on Mar 15, 2019

  1. cleaned up readme.md. New links, different genomes.

    @jasminelmah
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  2. cleaned up readme.md. New links, different genomes.

    @jasminelmah
    jasminelmah committed Mar 15, 2019
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  3. Found genome-derived prot seqs (Ensembl)

    @jasminelmah
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  4. Found genome-derived prot seqs (Ensembl)

    @jasminelmah
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  5. links to more animal genomes.

    @jasminelmah
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  6. links to more animal genomes.

    @jasminelmah
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Commits on Mar 16, 2019

  1. wrangling the pep fasta files. exhausting! ready to zzzzz.

    @jasminelmah
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  2. wrangling the pep fasta files. exhausting! ready to zzzzz.

    @jasminelmah
    jasminelmah committed Mar 16, 2019
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  3. just kidding! I'm back! made the agalma scripts - ready to run. NOW t… 

    …ime to sleep
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  4. just kidding! I'm back! made the agalma scripts - ready to run. NOW t… 

    …ime to sleep
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Commits on Mar 17, 2019

  1. realized need only 1 pep seq per gene. RE-search strikes againgit add… 

    … .! >:(
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  2. realized need only 1 pep seq per gene. RE-search strikes againgit add… 

    … .! >:(
    @jasminelmah
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  3. code to select longest pep and print list of names of longest peps.

    @jasminelmah
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  4. code to select longest pep and print list of names of longest peps.

    @jasminelmah
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Commits on Mar 20, 2019

  1. reformatted all pep fasta names so that it can actually be read by my… 

    … longest pep script.
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  2. reformatted all pep fasta names so that it can actually be read by my… 

    … longest pep script.
    @jasminelmah
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  3. added fasta puller program

    @jasminelmah
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  4. added fasta puller program

    @jasminelmah
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Commits on Mar 21, 2019

  1. FINALLY managed to make fastas of longest pep only. Submitted 01-impo… 

    …rt_compgen to farnam. Hooray
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  2. FINALLY managed to make fastas of longest pep only. Submitted 01-impo… 

    …rt_compgen to farnam. Hooray
    @jasminelmah
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  3. decided to send in agalma with no hydra - can anticipate trouble pars… 

    …ing hydra gff3s.
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  4. added no hydra agalma script b/c. A lot of trouble trying ot parse it… 

    …s weird gff3 files.
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  5. trying to resolve conflict.

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    jasminelmah committed Mar 21, 2019
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  6. healing git commits

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  7. r code to parse out gene_id from attributes column of gff3s

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Commits on Mar 23, 2019

  1. agalma homology sql csvs added

    @jasminelmah
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  2. close to completing code for master table. just need to figure out ho… 

    …w to indicate animal id, which is not given in any of the files :-/
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  3. found row num coordinates for each animal.

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  4. added animal column to final.master.table. phew.

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  5. I think I am finished master table?

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  6. Ok NOW we are probably finished final master table.

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Commits on Mar 25, 2019

  1. writing code for clustering

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Commits on Mar 26, 2019

  1. first run clustering with agnes. creates dendrogram. how to cut?

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  2. crossclustering working but can't figure out how to find cluster no.-… 

    …scaffold ID :(.
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Commits on Mar 30, 2019

  1. quick save

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Commits on Mar 31, 2019

  1. save some measely progress

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    jasminelmah committed Mar 31, 2019
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  2. anti_join to find absent homology_ids

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    jasminelmah committed Mar 31, 2019
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Commits on Apr 1, 2019

  1. some confused code.

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    jasminelmah committed Apr 1, 2019
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  2. looping issue.

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    jasminelmah committed Apr 1, 2019
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  3. more confused coding

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    jasminelmah committed Apr 1, 2019
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  4. seemingly have analysis working w/ sample data.

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    jasminelmah committed Apr 1, 2019
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Commits on Apr 9, 2019

  1. added species indices

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    jasminelmah committed Apr 9, 2019
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Commits on Apr 10, 2019

  1. fixed later diverging gene problem

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    jasminelmah committed Apr 10, 2019
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  2. played with tsne plot

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    jasminelmah committed Apr 10, 2019
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Commits on Apr 11, 2019

  1. sleuthing over reduction in scaffold numbers.

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    jasminelmah committed Apr 11, 2019
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Commits on Apr 13, 2019

  1. quick save before start screwing around

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    jasminelmah committed Apr 13, 2019
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  2. everything is broken! :( and that's how the day is going.

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    jasminelmah committed Apr 13, 2019
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Commits on Apr 14, 2019

  1. 5taxa still did not work. subset data. playing around with distance m… 

    …etrics for sparse data.
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    jasminelmah committed Apr 14, 2019
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Commits on Apr 16, 2019

  1. modified scaffold length script

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    jasminelmah committed Apr 16, 2019
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  2. working on graphs

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    jasminelmah committed Apr 16, 2019
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  3. progress making graphs

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    jasminelmah committed Apr 16, 2019
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Commits on Apr 17, 2019

  1. save progress on talk

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    jasminelmah committed Apr 17, 2019
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  2. talk progress

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    jasminelmah committed Apr 17, 2019
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Commits on Apr 18, 2019

  1. talk progress

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    jasminelmah committed Apr 18, 2019
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  2. more talk progress

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    jasminelmah committed Apr 18, 2019
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  3. talk prep

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    jasminelmah committed Apr 18, 2019
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  4. final talk version

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    jasminelmah committed Apr 18, 2019
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Commits on Apr 20, 2019

  1. null hypothesis graphs complete.

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    jasminelmah committed Apr 20, 2019
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  2. working on code file

    @jasminelmah
    jasminelmah committed Apr 20, 2019
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  3. added genome stats code to code.md but can't figure out how to save p… 

    …lots while looping.
    @jasminelmah
    jasminelmah committed Apr 20, 2019
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  4. more progress on code.md

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    jasminelmah committed Apr 20, 2019
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  5. save progress on code.md

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    jasminelmah committed Apr 20, 2019
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  6. chugging along

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    jasminelmah committed Apr 20, 2019
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  7. small tweak

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    jasminelmah committed Apr 20, 2019
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Commits on Apr 21, 2019

  1. save before changing all the variable names

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    jasminelmah committed Apr 21, 2019
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  2. save progress before screwing around with clustering section

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    jasminelmah committed Apr 21, 2019
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  3. broke cluster code, then (I think) fixed cluster code. Now broke abse… 

    …nce analysis code. -_-
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    jasminelmah committed Apr 21, 2019
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Commits on Apr 22, 2019

  1. finally fixed absence analysis. when making master table at end of cl… 

    …uster analysis, used already-filtered gff3.table, when needed unfiltered. This meant that all sequences other than comparison animal seqs had species_index > comp.species.index
    @jasminelmah
    jasminelmah committed Apr 22, 2019
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  2. mostly finished methods section, barring some cleaning. dinner time.

    @jasminelmah
    jasminelmah committed Apr 22, 2019
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  3. notes

    @jasminelmah
    jasminelmah committed Apr 22, 2019
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  4. trying to embed pics into readme

    @jasminelmah
    jasminelmah committed Apr 22, 2019
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  5. reconfigure methods

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    jasminelmah committed Apr 22, 2019
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  6. save before embarking on tree manip attempt

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    jasminelmah committed Apr 22, 2019
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  7. puzzling through tree approach

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    jasminelmah committed Apr 22, 2019
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  8. progress on tree approach

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    jasminelmah committed Apr 22, 2019
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Commits on Apr 23, 2019

  1. set comparison in tree approach worked out

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    jasminelmah committed Apr 23, 2019
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  2. close to getting tree approach

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    jasminelmah committed Apr 23, 2019
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  3. tree approach complete. might want to make prettier table.

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    jasminelmah committed Apr 23, 2019
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  4. code.md updated.

    @jasminelmah
    jasminelmah committed Apr 23, 2019
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  5. updating code.md

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    jasminelmah committed Apr 23, 2019
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  6. progress on code.md

    @jasminelmah
    jasminelmah committed Apr 23, 2019
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  7. save progress

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    jasminelmah committed Apr 23, 2019
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Commits on Apr 25, 2019

  1. readme progress

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    jasminelmah committed Apr 25, 2019
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  2. more readme progress

    @jasminelmah
    jasminelmah committed Apr 25, 2019
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  3. time to sleep

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    jasminelmah committed Apr 25, 2019
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  4. having trouble ordering x-axis of med scaff len graph

    @jasminelmah
    jasminelmah committed Apr 25, 2019
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Commits on Apr 26, 2019

  1. inserting images.

    @jasminelmah
    jasminelmah committed Apr 26, 2019
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  2. adding images to code.md

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    jasminelmah committed Apr 26, 2019
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Commits on Apr 27, 2019

  1. rearranging and reformatting code.md

    @jasminelmah
    jasminelmah committed Apr 27, 2019
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  2. working on sample data for cleaned code

    @jasminelmah
    jasminelmah committed Apr 27, 2019
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  3. checking progress on readme, clean code.

    @jasminelmah
    jasminelmah committed Apr 27, 2019
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  4. cleaning up code

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    jasminelmah committed Apr 27, 2019
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  5. managed to break tree code. I think I fixed it now? :-/

    @jasminelmah
    jasminelmah committed Apr 27, 2019
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  6. extra note

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    jasminelmah committed Apr 27, 2019
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  7. add pylr library

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    jasminelmah committed Apr 27, 2019
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Commits on Apr 28, 2019

  1. running through clean code, cleaning up readme

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    jasminelmah committed Apr 28, 2019
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  2. code_clean.rmd runs through clean. don't touch it any more! changed n… 

    …eurogenes.rmd and code.md accordingly. no more touchy the code.
    @jasminelmah
    jasminelmah committed Apr 28, 2019
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  3. adjusting image sizes

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    jasminelmah committed Apr 28, 2019
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  4. mostly final version of repo.

    @jasminelmah
    jasminelmah committed Apr 28, 2019
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  5. final version?

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    jasminelmah committed Apr 28, 2019
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  6. just kidding

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    jasminelmah committed Apr 28, 2019
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  7. found some errors

    @jasminelmah
    jasminelmah committed Apr 28, 2019
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  8. tweaked wording

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    jasminelmah committed Apr 28, 2019
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Commits on Apr 30, 2019

  1. found bug - 100x100 subsample IS random, but ONLY sampled first 100 r… 

    …ows/columns meaning only Hsa and Dre was in matrix - not Spu. Corrected, but since Spu outnumbers Hsa and Dre by far clustering pattern is different. Repeating this workflow with Hsa Dre and Tgu leads to same clustering pattern as before. Is this clustering pattern unique to high quality genomes?
    @jasminelmah
    jasminelmah committed Apr 30, 2019
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