inst/extdata/README.md

In jianhong/ATACseqTFEA: Transcription Factor Enrichment Analysis for ATAC-seq

File list

Motifs saved in R objects.

• best_curated_Human.rds: The best_curated_Human is a list of TF motifs downloaded from TFEA github. There are 1279 human motifs in the data set.

• cluster_PWMs.rds: The cluster_PWMs is a list of non-redundant TF motifs downloaded from DeepSTARR. There are 6502 motifs in the data set.

• PWMatrixList.rds: The PWMatrixList is a collection of jasper2018, jolma2013 and cisbp_1.02 from package motifDB (v 1.28.0) and merged by distance smaller than 1e-9 calculated by MotIV::motifDistances function (v 1.42.0). The merged motifs were exported by motifStack (v 1.30.0).

Command line scripts

• sample_scripts.R: This script will run the TFEA step by step and save the intermediate results in R objects.

Unit test or documentation used R objects.

• bindingSites.rds: The sample outputs of the function prepareBindingSites
• res.rds: The sample outputs of the function TFEA

Sample bam files and their index files.

The bam files are insertion site shifted files. KD means Knockdown; WT means wild type.

• KD.shift.rep1.bam
• KD.shift.rep1.bam.bai
• KD.shift.rep2.bam
• KD.shift.rep2.bam.bai
• WT.shift.rep1.bam
• WT.shift.rep1.bam.bai
• WT.shift.rep2.bam
• WT.shift.rep2.bam.bai

jianhong/ATACseqTFEA documentation built on May 8, 2024, 2:06 a.m.