Ali Kishk, PhD

AmpliconNet: Sequence Based Multi-layer Perceptron for Amplicon Read Classification Using Real-time Data Augmentation

4

> Taxonomic assignment is the core of targeted metagenomics approaches that aims to assign sequencing reads to their corresponding taxonomy. Sequence similarity searching and machine learning (ML) are two commonly...

https://github.com/mims-harvard/decagon/blob/86ff6b1423e548c22cbb8f70c5dac22b79d45290/requirements.txt#L8

DeprecationWarning: Deprecated. Use gensim.models.KeyedVectors.load_word2vec_format instead.

2

https://github.com/pnpnpn/dna2vec/blob/8d033e9312ae3342491414a513bb1cf5d2944503/dna2vec/multi_k_model.py#L17

Trying to run doubleGeneDeeletion script on PALM.jl

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I have only both the model.mat and KO script 'Macrophage_KO.m' in the test directory. PALM(modelDir, "$(joinpath(dirname(pathof(COBRA)), "../test/Macrophage_KO.m"))", nMatlab=nWorkers, outputFile="modelCharacteristics.mat", varsCharact=varsCharact, cobraToolboxDir=installDir) but I am getting this error: >> Every worker...

Using ComBat-Seq over RSEM estimated counts

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Hi, I have 2 RNA-Seq studies on RSEM counts only. Would it a problem using the float RSEM counts as an input to ComBat-Seq? or Should I round them? Thanks...

Inference Problem

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with open("../../para-nmt-50m/data/ngram-word-concat-40.pickle", 'rb') as f: FileNotFoundError: [Errno 2] No such file or directory: '../../para-nmt-50m/data/ngram-word-concat-40.pickle'