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References from Seq-ing answers: Current data integration approaches to uncover mechanisms of transcriptional regulation. Local targets link to admitted publications; unresolved targets remain external evidence.
10.1101/gr.136184.111
10.1101/gr.136184.111 · External reference
ATAC-seq: a method for assaying chromatin accessibility genome-wide
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10.1016/j.cels.2016.10.019
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Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins
10.1073/pnas.1316064110 · 2013 · External reference
Substantial biases in ultra-short read data sets from high-throughput DNA sequencing
10.1093/nar/gkn425 · 2008 · External reference
10.1073/pnas.0905443106
10.1073/pnas.0905443106 · External reference
PeakSeq: systematic scoring of ChIP-Seq experiments relative to controls
10.1038/nbt.1518 · 2009 · External reference
10.1214/11-aoas466
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Empirical assessment of the impact of sample number and read depth on RNA-Seq analysis workflow performance
10.1186/s12859-018-2445-2 · 2018 · External reference
RNA-seq differential expression studies: more sequence or more replication?
10.1093/bioinformatics/btt688 · 2014 · External reference
Calculating sample size estimates for RNA sequencing data
10.1089/cmb.2012.0283 · 2013 · External reference
Power analysis and sample size estimation for RNA-Seq differential expression
10.1261/rna.046011.114 · 2014 · External reference
RnaSeqSampleSize: real data based sample size estimation for RNA sequencing
10.1186/s12859-018-2191-5 · 2018 · External reference
Sample size calculation based on generalized linear models for differential expression analysis in RNA-seq data
10.1515/sagmb-2016-0008 · 2016 · External reference
PROPER: comprehensive power evaluation for differential expression using RNA-seq
10.1093/bioinformatics/btu640 · 2015 · External reference
Feasibility of sample size calculation for RNA-seq studies
2018 · External reference
10.1073/pnas.51.5.786
10.1073/pnas.51.5.786 · External reference
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CUT&Tag for efficient epigenomic profiling of small samples and single cells
2019 · External reference
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2011 · External reference
10.1093/bioinformatics/btp324
10.1093/bioinformatics/btp324 · External reference
10.1186/gb-2009-10-3-r25
10.1186/gb-2009-10-3-r25 · External reference
10.1186/gb-2008-9-9-r137
10.1186/gb-2008-9-9-r137 · External reference
histoneHMM: Differential analysis of histone modifications with broad genomic footprints
10.1186/s12859-015-0491-6 · 2015 · External reference
Features that define the best ChIP-seq peak calling algorithms
2017 · External reference
10.1371/journal.pcbi.1002613
10.1371/journal.pcbi.1002613 · External reference
10.1186/s13059-014-0474-3
10.1186/s13059-014-0474-3 · External reference
10.1186/s13072-019-0287-4
10.1186/s13072-019-0287-4 · External reference
Recent advances in ChIP-seq analysis: from quality management to whole-genome annotation
2017 · External reference
Accounting for immunoprecipitation efficiencies in the statistical analysis of ChIP-seq data
10.1186/1471-2105-14-169 · 2013 · External reference
10.1007/s40484-017-0111-8
10.1007/s40484-017-0111-8 · External reference
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
10.1093/bioinformatics/btp616 · 2010 · External reference
10.1186/gb-2010-11-10-r106
10.1186/gb-2010-11-10-r106 · External reference
csaw: a Bioconductor package for differential binding analysis of ChIP-seq data using sliding windows
2016 · External reference
10.1186/gb-2012-13-3-r16
10.1186/gb-2012-13-3-r16 · External reference
10.1038/nbt.1754
10.1038/nbt.1754 · External reference
10.1093/nar/gkg129
10.1093/nar/gkg129 · External reference
10.1038/nbt.1630
10.1038/nbt.1630 · External reference
10.1186/1471-2105-11-237
10.1186/1471-2105-11-237 · External reference
10.1093/bioinformatics/btv145
10.1093/bioinformatics/btv145 · External reference
10.1038/nature09380
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10.1016/j.cell.2017.02.007
10.1016/j.cell.2017.02.007 · External reference
Promoter capture Hi-C: high-resolution, genome-wide profiling of promoter interactions
10.3791/57320 · 2018 · External reference
10.1146/annurev-genom-082908-145957
10.1146/annurev-genom-082908-145957 · External reference
10.1111/1755-0998.12109
10.1111/1755-0998.12109 · External reference
10.1016/j.csbj.2019.04.012 · Admitted local publication
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10.1093/bioinformatics/bts635 · External reference
10.1093/bioinformatics/btp120
10.1093/bioinformatics/btp120 · External reference
10.1186/gb-2013-14-4-r36
10.1186/gb-2013-14-4-r36 · External reference
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10.1038/nbt.3519 · External reference
10.1038/nmeth.4197
10.1038/nmeth.4197 · External reference
10.1186/1471-2105-12-323
10.1186/1471-2105-12-323 · External reference
10.1111/mec.12014
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10.1038/nature08872
10.1038/nature08872 · External reference
10.1186/gb-2011-12-3-r22
10.1186/gb-2011-12-3-r22 · External reference
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
10.1093/bioinformatics/btt656 · 2014 · External reference
Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments
10.1186/1471-2105-11-94 · 2010 · External reference
A comparison of per sample global scaling and per gene normalization methods for differential expression analysis of RNA-seq data
10.1371/journal.pone.0176185 · 2017 · External reference
10.1093/nar/gks001
10.1093/nar/gks001 · External reference
10.1038/nrg3642
10.1038/nrg3642 · External reference
10.1101/gr.124321.111
10.1101/gr.124321.111 · External reference
Selecting between-sample RNA-Seq normalization methods from the perspective of their assumptions
10.1093/bib/bbx008 · 2017 · External reference
10.1093/bib/bbs046
10.1093/bib/bbs046 · External reference
10.1038/nmeth.1226
10.1038/nmeth.1226 · External reference
A scaling normalization method for differential expression analysis of RNA-seq data
2010 · External reference
The impact of quality control in RNA-seq experiments
10.1088/1742-6596/705/1/012003 · 2016 · External reference
10.1093/bioinformatics/btw313
10.1093/bioinformatics/btw313 · External reference
10.1093/biostatistics/kxr031
10.1093/biostatistics/kxr031 · External reference
10.1101/gr.7.10.986
10.1101/gr.7.10.986 · External reference
Genetic variants contribute to gene expression variability in humans
10.1534/genetics.112.146779 · 2013 · External reference
10.1093/bioinformatics/btr616
10.1093/bioinformatics/btr616 · External reference
10.1186/s13059-014-0550-8
10.1186/s13059-014-0550-8 · External reference
Small-sample estimation of negative binomial dispersion, with applications to SAGE data
10.1093/biostatistics/kxm030 · 2008 · External reference
10.1093/nar/gks042
10.1093/nar/gks042 · External reference
10.1093/nar/gku310
10.1093/nar/gku310 · External reference
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10.1038/nbt.2957
10.1038/nbt.2957 · External reference
10.1073/pnas.0506580102
10.1073/pnas.0506580102 · External reference
The ontology of the gene ontology
2003 · External reference
10.1038/nprot.2008.211
10.1038/nprot.2008.211 · External reference
10.1093/nar/gkn923
10.1093/nar/gkn923 · External reference
10.1093/nar/28.1.27
10.1093/nar/28.1.27 · External reference
Reactome pathway analysis: a high-performance in-memory approach
10.1186/s12859-017-1559-2 · 2017 · External reference
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10.1371/journal.pone.0006447 · External reference
10.1038/nrg3433
10.1038/nrg3433 · External reference
Inferring interaction networks from multi-omics data
2019 · External reference
10.1093/nar/gkt1115
10.1093/nar/gkt1115 · External reference
10.1093/nar/gky1131
10.1093/nar/gky1131 · External reference
10.1093/nar/gky1079
10.1093/nar/gky1079 · External reference
10.1093/bib/bbs016
10.1093/bib/bbs016 · External reference
10.1016/j.molcel.2010.05.004
10.1016/j.molcel.2010.05.004 · External reference
MEME-ChIP: motif analysis of large DNA datasets
10.1093/bioinformatics/btr189 · 2011 · External reference
10.1093/nar/gku1083
10.1093/nar/gku1083 · External reference
10.1093/nar/gkt997
10.1093/nar/gkt997 · External reference
10.1016/j.cell.2014.08.009
10.1016/j.cell.2014.08.009 · External reference
10.1093/nar/gkx1106
10.1093/nar/gkx1106 · External reference
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10.1038/47412 · External reference
10.1038/nbt.1662
10.1038/nbt.1662 · External reference
10.1093/bioinformatics/btn627
10.1093/bioinformatics/btn627 · External reference
10.1093/nar/gks461
10.1093/nar/gks461 · External reference
10.1038/nprot.2013.150
10.1038/nprot.2013.150 · External reference
10.1101/gr.136838.111
10.1101/gr.136838.111 · External reference
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10.1073/pnas.0909344107 · External reference
Integrated analysis of motif activity and gene expression changes of transcription factors
10.1101/gr.227231.117 · 2018 · External reference
10.1101/pdb.prot5384
10.1101/pdb.prot5384 · External reference
10.1038/nmeth.2688
10.1038/nmeth.2688 · External reference
10.1101/gr.112656.110
10.1101/gr.112656.110 · External reference
10.1101/gr.135129.111
10.1101/gr.135129.111 · External reference
10.1093/nar/gkw1061
10.1093/nar/gkw1061 · External reference
10.1101/gr.112623.110
10.1101/gr.112623.110 · External reference
10.1093/bioinformatics/btu519
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10.1186/s13059-019-1642-2
10.1186/s13059-019-1642-2 · External reference
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10.1038/s41576-019-0122-6 · External reference
10.1038/nmeth.3547
10.1038/nmeth.3547 · External reference
10.1038/nbt.3300
10.1038/nbt.3300 · External reference
10.1038/s41588-018-0160-6
10.1038/s41588-018-0160-6 · External reference
Deep learning at base-resolution reveals motif syntax of the cis-regulatory code
2019 · External reference
10.1016/j.cell.2016.11.038
10.1016/j.cell.2016.11.038 · External reference
scMAGeCK links genotypes with multiple phenotypes in single-cell CRISPR screens
10.1186/s13059-020-1928-4 · 2020 · External reference
10.1126/science.1232542
10.1126/science.1232542 · External reference
Interrogation of enhancer function by enhancer-targeting CRISPR epigenetic editing
2020 · External reference