Pathways#13

Open

lucasfein wants to merge 201 commits intoversion1from

Commits on Nov 7, 2018

pathway queries, local consensusdb
lucasfein
committed
dict entry fix
lucasfein
committed
resetting wikipathways
lucasfein
committed
resetting wikipathways
lucasfein
committed
resetting wikipathways
lucasfein
committed
wikipathways as submodule
lucasfein
committed

Commits on Nov 8, 2018

consensus path db automated update, get_pathways()
lucasfein
committed
exclude directly queried databases from cpdb
lucasfein
committed
clearer list uniquification
lucasfein
committed
more efficient result output
lucasfein
committed
removed unnecessary conversion
lucasfein
committed

Commits on Nov 9, 2018

building pathway db
lucasfein
committed
pathway db
lucasfein
committed
pathway db
lucasfein
committed
Merge pull request #7 from Genome3d/lucas
Lucas Fein
authored

Commits on Nov 11, 2018

Merge pull request #8 from Genome3d/lucas
Lucas Fein
authored

Commits on Nov 13, 2018

wikipathways edit
lucasfein
committed
wikipathways
lucasfein
committed
improvements regarding robustness
lucasfein
committed
naming
lucasfein
committed
secure encoding
lucasfein
committed
return produce_summary()
lucasfein
committed
ConnectionError
lucasfein
committed
ConnectionError Wikipathways specific
lucasfein
committed
encoding incompatibilities
lucasfein
committed

Commits on Nov 14, 2018

logging
lucasfein
committed
minor changes, logging, typos
lucasfein
committed
fixed timeout handling
lucasfein
committed
fixed timeout handling
lucasfein
committed
handling ConnectionError
lucasfein
committed
pathway summary integration
lucasfein
committed
run pathway summary separately
lucasfein
committed

Commits on Nov 22, 2018

wikipathways as forked submodule, significant expression variation across tissues within pathways
lucasfein
committed
tracking master
lucasfein
committed
removed submodule
lucasfein
committed
wikipathways on branch master
lucasfein
committed
wikipathways track master
lucasfein
committed
wikipathways at master
lucasfein
committed
removed submodule
lucasfein
committed
wikipathways on master
lucasfein
committed
saving to dict, no output files
lucasfein
committed

Commits on Nov 26, 2018

gene expression z-scores mapped to pathways - current state
lucasfein
committed

Commits on Nov 29, 2018

no wp api client needed
lucasfein
committed

Commits on Nov 30, 2018

up/downstream for wikipathways
lucasfein
committed

Commits on Dec 5, 2018

up/downstream for reactome, queries robust via requests not pycurl
lucasfein
committed
relocated file io setup to function
lucasfein
committed

Commits on Dec 6, 2018

code relocated to main file
lucasfein
committed

Commits on Dec 12, 2018

Commits on Dec 13, 2018

Commits on Dec 14, 2018

reduced queries for kegg
lucasfein
committed
reduced queries for kegg
lucasfein
committed

Commits on Dec 15, 2018

wikipathways: hard coding namespace map
lucasfein
committed

Commits on Dec 17, 2018

csv writing improved
lucasfein
committed
csv writing
lucasfein
committed

Commits on Dec 18, 2018

wp: excluding metabolites from interactions/expression integration
lucasfein
committed

Commits on Dec 19, 2018

HPM Protein Expression Data integrated
lucasfein
committed

Commits on Jan 6, 2019

wp: gene products only as up/downstream, hpm: peptide and gene level
lucasfein
committed

Commits on Jan 7, 2019

argument order fixed
lucasfein
committed
hpm: fixes, file names as in original data set
lucasfein
committed
summary: overview of set sizes during multiprocessing, pathway_summary prepared
lucasfein
committed

Commits on Jan 8, 2019

logging: number of genes queried etc
lucasfein
committed
pathway summary: snp-gene mappings
lucasfein
committed
HTML parsing error altered
lucasfein
committed
multiprocessing db queries
lucasfein
committed

Commits on Jan 11, 2019

pathway summary
lucasfein
committed

Commits on Jan 14, 2019

pathway summary
lucasfein
committed
rebased added wikipathways
lucasfein
committed
reduced globals
lucasfein
committed
removed globals
lucasfein
committed
beginning pathway integration
lucasfein
committed
pathway query
lucasfein
committed
unecessary import
lucasfein
committed
formatting
lucasfein
committed
clean up, preparation for pull
lucasfein
committed
produce_summary() return
lucasfein
committed
shebang
lucasfein
committed
alphabetic order unecessary
lucasfein
committed
alphabetic order unecessary
lucasfein
committed
dict iteration fix
lucasfein
committed
pathway import not necessary
lucasfein
committed
cell lines ordered
lucasfein
committed
pathway queries, local consensusdb
lucasfein
committed
dict entry fix
lucasfein
committed
resetting wikipathways
lucasfein
committed
resetting wikipathways
lucasfein
committed
resetting wikipathways
lucasfein
committed
wikipathways as submodule
lucasfein
committed
consensus path db automated update, get_pathways()
lucasfein
committed
exclude directly queried databases from cpdb
lucasfein
committed
clearer list uniquification
lucasfein
committed
more efficient result output
lucasfein
committed
removed unnecessary conversion
lucasfein
committed
building pathway db
lucasfein
committed
Revert "clearer list uniquification"
lucasfein
committed
pathway db
lucasfein
committed
robust against missing genes.txt
lucasfein
committed
code style
lucasfein
committed
code style
lucasfein
committed
wikipathways edit
lucasfein
committed
wikipathways
lucasfein
committed
improvements regarding robustness
lucasfein
committed
naming
lucasfein
committed
secure encoding
lucasfein
committed
return produce_summary()
lucasfein
committed
ConnectionError
lucasfein
committed
ConnectionError Wikipathways specific
lucasfein
committed
encoding incompatibilities
lucasfein
committed
logging
lucasfein
committed
minor changes, logging, typos
lucasfein
committed
fixed timeout handling
lucasfein
committed
fixed timeout handling
lucasfein
committed
handling ConnectionError
lucasfein
committed
pathway summary integration
lucasfein
committed
run pathway summary separately
lucasfein
committed
wikipathways as forked submodule, significant expression variation across tissues within pathways
lucasfein
committed
tracking master
lucasfein
committed
removed submodule
lucasfein
committed
wikipathways on branch master
lucasfein
committed
wikipathways track master
lucasfein
committed
wikipathways at master
lucasfein
committed
removed submodule
lucasfein
committed
wikipathways on master
lucasfein
committed
saving to dict, no output files
lucasfein
committed
gene expression z-scores mapped to pathways - current state
lucasfein
committed
no wp api client needed
lucasfein
committed
up/downstream for wikipathways
lucasfein
committed
up/downstream for reactome, queries robust via requests not pycurl
lucasfein
committed
relocated file io setup to function
lucasfein
committed
code relocated to main file
lucasfein
committed
up/downstream for kegg, pathway versions for kegg, db version for wikipathways
lucasfein
committed
robustness regarding input/style/processing input line by line
lucasfein
committed
robustness: kegg: gene exists but has no pathways associated
lucasfein
committed
robustness: previously unknown tag in wp interaction xml/reactome: posttranslational modification in protein ids stripped
lucasfein
committed
reduced queries for kegg
lucasfein
committed
reduced queries for kegg
lucasfein
committed
wikipathways: hard coding namespace map
lucasfein
committed
csv writing improved
lucasfein
committed
csv writing
lucasfein
committed
wp: excluding metabolites from interactions/expression integration
lucasfein
committed
HPM Protein Expression Data integrated
lucasfein
committed
wp: gene products only as up/downstream, hpm: peptide and gene level
lucasfein
committed
argument order fixed
lucasfein
committed
hpm: fixes, file names as in original data set
lucasfein
committed
summary: overview of set sizes during multiprocessing, pathway_summary prepared
lucasfein
committed
logging: number of genes queried etc
lucasfein
committed
pathway summary: snp-gene mappings
lucasfein
committed
HTML parsing error altered
lucasfein
committed
multiprocessing db queries
lucasfein
committed
pathway summary
lucasfein
committed
pathway summary
lucasfein
committed
Merge branch 'pathways' of https://github.com/Genome3d/codes3d-v1 into pathways
lucasfein
committed
fixes
lucasfein
committed
kegg: limiting URL length; wikipathways: curation tags
lucasfein
committed

Commits on Jan 15, 2019

wp: handling of broken gpml gene names
lucasfein
committed

Commits on Jan 16, 2019

react: specificity of stripping modfications via regex
lucasfein
committed
wp: capitalizing gene names according to hgnc
lucasfein
committed
fixed naming problem
lucasfein
committed
wp: excluding homology mappings
lucasfein
committed
wp: only gene names with xref
lucasfein
committed

Commits on Jan 17, 2019

wp: regex modifications
lucasfein
committed
reactome: different access; comments
lucasfein
committed

Commits on Jan 18, 2019

cleaned up using class
lucasfein
committed

Commits on Jan 22, 2019

one buffer size, 2 threads per process
lucasfein
committed
altered reactome query, gene name correction
lucasfein
committed
kegg: robust against failing queries
lucasfein
committed

Commits on Jan 23, 2019

wp: up/down regulation
lucasfein
committed

Commits on Jan 24, 2019

expression data
lucasfein
committed
wp only
lucasfein
committed
print gene_ids removed
lucasfein
committed

Commits on Jan 25, 2019

gene synonym mapping
lucasfein
committed
dynamic nsmap
lucasfein
committed
GTEX integration
lucasfein
committed

Commits on Jan 26, 2019

gtex integration
lucasfein
committed
gtex
lucasfein
committed

Commits on Jan 29, 2019

gene synonyms: efficient handling
lucasfein
committed
naming error
lucasfein
committed
pathway summary
lucasfein
committed
more gene remapping, hpm: gene 0 => prot 0
lucasfein
committed

Commits on Jan 30, 2019

pathway queries and summary changes
lucasfein
committed

Commits on Jan 31, 2019

plots phosphorylation
lucasfein
committed

Commits on Feb 5, 2019

merged, retry requests
lucasfein
committed
misc dir removed
lucasfein
committed
gitignore updated
lucasfein
committed
logging
lucasfein
committed

Commits on Feb 7, 2019

sqllite queries, heatmap layout
lucasfein
committed
heatmap layout
lucasfein
committed

Commits on Feb 10, 2019

plots: p added
lucasfein
committed

Commits on Feb 13, 2019

optional numbers
lucasfein
committed

Commits on Feb 15, 2019

clustering
lucasfein
committed

Commits on Mar 2, 2019

gene-only mode; legend
lucasfein
committed

Commits on Mar 3, 2019

integration
lucasfein
committed
merge conflicts addressed
lucasfein
committed
Merge pull request #12 from Genome3d/pathways_to_version1
Lucas Fein
authored
merge conflict in produce summary
lucasfein
committed

Commits on Mar 6, 2019

fixed integration problems
lucasfein
committed

Commits on Mar 7, 2019

integration issue, global class
lucasfein
committed

Commits on Mar 9, 2019

clustering genes only when 3 or more
lucasfein
committed

Commits on Apr 10, 2019

Merge branch 'version1' into pathways
Lucas Fein
authored
static wspace
Lucas Fein
authored