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Missing citation - 17.3 #69

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katiem221 opened this issue Oct 30, 2024 · 0 comments
Open

Missing citation - 17.3 #69

katiem221 opened this issue Oct 30, 2024 · 0 comments
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katiem221 commented Oct 30, 2024

Describe what is not working with the course

Section 17.3 is missing a citation:
'The TSS enrichment score in ATAC-seq measures the preferential accessibility of chromatin regions near gene promoters. This approach was established in pipelines for bulk ATAC-seq, such as the ENCODE pipeline (cite)'

17.4:
'Peak calling in ATAC-seq is performed in a similar manner to bulk ATAC-seq [ref bulk chapter].'
'Peak calling is commonly performed using MACS2, but other peak callers suitable for ATAC-seq could be used as well, as described in our chapter on bulk ATAC-seq (reference).'

17.13:
'The distinct approaches of the tools discussed here lead to varying levels of performance on different types of data, and extensive benchmarking has been performed (here) and (here) on synthetic datasets to determine the accuracy of different approaches'

17.16:
'A comprehensive explanation of packages to convert between single-cell data object types used by Python and R packages is found here.'

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