xguse / blacktie
Blacktie: a streamlined interface to the popular tophat/cufflinks RNA-seq pipeline
☆26Updated 9 years ago
Alternatives and similar repositories for blacktie:
Users that are interested in blacktie are comparing it to the libraries listed below
- Modeling and correcting fragment sequence bias for RNA-seq☆24Updated 10 months ago
- Benchmarks for RNA-seq quantification pipelines☆8Updated 5 years ago
- Hotspot is a program for identifying genomic regions of local enrichment of short-read sequence tags.☆14Updated 11 years ago
- Improved multi-sample transcript abundance estimates using adaptive priors☆20Updated 6 years ago
- Normalization and difference calling for Next Generation Sequencing (NGS) data via joint multinomial modeling.☆11Updated 3 years ago
- A python script used to annotate genomic intervals.☆18Updated 4 years ago
- ☆12Updated last week
- R package to quickly obtain count vectors from indexed bam files☆15Updated 3 years ago
- Chromatin segmentation in R☆19Updated 7 years ago
- A curated list of awesome clonality and tumor heterogeneity resources☆15Updated 5 years ago
- Machine learning use cases for teaching☆13Updated 7 years ago
- Scripts for reproducing analyses of large RNA-seq datasets☆15Updated 5 years ago
- Qtip: a tandem simulation approach for accurately predicting read alignment mapping qualities☆25Updated 5 years ago
- Color DNA/RNA bases in terminal output☆21Updated 7 years ago
- XL-mHG: A Semiparametric Test for Enrichment in Ranked Lists.☆13Updated 2 years ago
- Mostly deprecated in favor of : https://github.com/hbc/bcbioRNASeq. Quality control, differential gene/transcript expression and pathway …☆24Updated 7 years ago
- R Interface to the NCBI SRA metadata☆23Updated 6 years ago
- A Feature Density Estimator for High-Throughput Sequence Tags☆23Updated 3 years ago
- RNF framework for NGS: simulation of reads, evaluation of mappers, conversion of RNF-compliant data.☆14Updated 6 years ago
- A tool for Read Multi-Mapper Resolution☆23Updated 8 years ago
- A hierarchical multiscale model for inferring transcription factor binding from chromatin accessibility data.☆26Updated 8 years ago
- ☆12Updated 4 months ago
- Expectation-Maximization algorithm for Allele-Specific Expression☆21Updated last year
- Correctly counting molecules using unique molecular identifiers (UMIs)☆9Updated 3 years ago
- ☆10Updated 9 years ago
- Reproducible reanalysis of a combined ChIP-Seq & RNA-Seq data set☆16Updated 5 years ago
- A Practical (And Opinionated) Guide To Analyzing 450K Data☆35Updated 10 years ago
- ChIP-seq peak calling with GC effects adjustment☆9Updated 6 years ago
- Peakzilla is a self-learning algorithm to identify transcription factor binding sites from ChIP-seq data. I would be very happy if you tr…☆20Updated last year
- Examples of kallisto + sleuth☆11Updated 7 years ago