Joris van Steenbrugge Jorisvansteenbrugge
Jorisvansteenbrugge
/ gist:3f55fab7475e81e00db81989a85decf9
Created
July 12, 2023 12:36
lg blocklist
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Jorisvansteenbrugge
/ ctr functions
Created
July 5, 2017 13:15
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| Apriori : Formal class 'refObjectGenerator' [package "methods"] with 4 slots | |
| array_fig : function (array, module, xlimits, ylimits, | |
| background, cluster_results) | |
| ave_Z_score_Func : function (combined_scores_array) | |
| Background_Distribution_Modules : function (RNAseq_Annotated_Matrix, matrix_features, | |
| Z_scores, N, Z, P = 2, range) | |
| Calc_Jaccard : function (vector1, vector2) | |
| Calc_Norm_Euc : function (vector1, vector2) | |
| calc_Z_scores : function (I_KOs_Background) | |
| cluster_func : function (RNAseq_Annotated_Matrix, pairwise_KO_distances, |
Jorisvansteenbrugge
/ transmissions.py
Created
June 12, 2017 11:04
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| def _transmission_probabilities(self, sequences): | |
| """ | |
| Missing: im, dd, ii | |
| """ | |
| self.t_mm[0], self.t_mi[0], \ | |
| self.t_md[0], self.t_im[0] = self._pos_prob(sequences, 0) | |
| self.t_mm[-1], self.t_mi[-1], \ | |
| self.t_md[-1], self.t_im[-1] = self._pos_prob(sequences, -1) |
Jorisvansteenbrugge
/ assignment2_joris.py
Created
May 31, 2017 18:52
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| #!/usr/bin/env python | |
| """ | |
| Author: Joris van Steenbrugge | |
| Student number: 950416798110 | |
| Implementation of the SSAHA algorithm | |
| """ | |
| from sys import argv, exit | |
| from Bio import SeqIO |
Jorisvansteenbrugge
/ annotatedKOterms.csv
Created
May 29, 2017 06:52
We can make this file beautiful and searchable if this error is corrected: It looks like row 7 should actually have 1 column, instead of 2 in line 6.
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| KOterm;Name;Definition | |
| K07473;dinJ;DNA-damage-inducible protein J | |
| K19157;yafQ;mRNA interferase YafQ | |
| K15726;czcA;cobalt-zinc-cadmium resistance protein CzcA | |
| K07807;K07807;uncharacterized protein | |
| K01534;zntA;Cd2+/Zn2+-exporting ATPase | |
| K15725;czcC;outer membrane protein, cobalt-zinc-cadmium efflux system | |
| K15727;czcB;membrane fusion protein, cobalt-zinc-cadmium efflux system | |
| K03496;parA, soj;chromosome partitioning protein | |
| K03101;lspA;signal peptidase II |