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"[75] Bathurst_Inlet was analyzed with a 1 \u00d7 5 ChemCam linescan and in two locations by APXS.",
"[98] 3. Bathurst_Inlet is enriched in Li and several locations show a marked decrease in Li with depth.",
"Another unique feature of Bathurst_Inlet is its relatively high Li (>30 ppm) at each of the five analysis points.",
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"[94] Preliminary Rb, Sr, and Ba trace element concentrations for three rocks, Jake_M, Bathurst_Inlet, and Et Then, and one soil, Portage, were analyzed by fitting the APXS spectra using the computer code GUAPX.",
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2026-04-05 06:45:29
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"CellMix implements in particular the method Digital Sorting Algorithm (DSA) proposed by Zhong et al. [21] which performs complete gene expression deconvolution using a set of marker genes only.",
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"CellMix implements in particular the method Digital Sorting Algorithm ( DSA) proposed by Zhong et al. [99] which performs complete gene expression deconvolution using a set of marker genes only.",
"Here, we used the R package CellMix (CellMix 1 .6.2, ), to estimate the proportions of the three tissue compartments in our tooth germ transcriptomes.",
"Here, we used the R package CellMix (CellMix, version 1.6.2,",
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2026-04-05 06:45:28
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"I used DESeq2 [Love et al. , 2014] to extract the \"timer genes\", which are genes that linearly increase/decrease over time, with at least a two-fold change between DE14.5 and ED18.",
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"Pour cela, j'ai extrait les informations de dispersion estim\u00e9es par DESeq2 au cours de l'analyse des g\u00e8nes DE BL pour la molaire sup\u00e9rieure et la molaire inf\u00e9rieure s\u00e9par\u00e9ment.",
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"J'ai d\u00e9fini ces g\u00e8nes \"timers\" \u00e0 partir du jeu de donn\u00e9e large \u00e9chelle souris, en r\u00e9alisant une analyse de g\u00e8nes DE, \u00e0 l'aide de DESeq2.",
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"Cela tient certainement \u00e0 l'estimation \u00e0 la hausse des g\u00e8nes faiblement exprim\u00e9 dans l'analyse Kallisto, ce qui n'est pas pr\u00e9vu par les lois statistiques utilis\u00e9es par le paquet DESeq2 [Love et al. , 2014] pour identifier les g\u00e8nes diff\u00e9rentiellement exprim\u00e9s, causant ainsi un biais dans la normalisation des donn\u00e9es et l'estimation des g\u00e8nes DE.",
"Using differential expression analysis, we find 8,387 genes that vary significantly according to the species, which is much more than the 130 genes that vary according to the upper/lower difference (DESeq2 analysis taking development stage into account, adjusted p-value <0.1).",
"J'ai pu observer que les deux m\u00e9thodes donnaient le m\u00eame signal de PCA, cependant ces m\u00e9thodes diff\u00e8rent dans l'estimation des enrichissements des g\u00e8nes diff\u00e9rentiellement exprim\u00e9s (obtenu par une analyse DESeq2 [Love et al. , 2014]).",
"We artificially increased the dispersion in upper libraries using dispersion law of lower molars (from DESeq2 analysis) or we artificially decreased dispersion in lower library using dispersion law of upper molar (from DESeq2 analysis), in both cases we still found more genes DE in upper molars.",
"This was indeed the case when taking genes that vary significantly during development, in a linear manner (comparison of 3,281 genes whose expression level is increasing linearly, with 3,181 genes which are decreasing linearly : Wilcoxon test, Pvalue < 10-16; DE-genes with a significant time-related bias, adjusted P-value < 0.05, DESeq2)."
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2026-04-05 06:45:28
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"R scripts corresponding to the main methods and processed data are available on GitHub (https: // github. com/ msemon/ ToothTranscriptomeAnalyses ) [87] and in zenodo (doi:10.5281/zenodo.197077).",
"Comparable sequences for 10,516 pairs of orthologous genes were extracted by an automated and accurate pipeline (Amalgam, GitHub https://github.com/CarineRey/",
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