- Samtools variant caller for each individual sample
- CAGEFightR to get CTSS from CAGE error
- Around 3 months short course or summer school in Bioinformatics
- Salmon tximport get TPM
- Extracting important gene with similar expression level from multiple samples
- FIMO score calculation
- FASTQ alignment result is really bad
- Transcript differential exprs analysis using Kallisto not significant
- Bedtools with name and full header
- Bismark duplicate ID error
- VCF file period symbol in the genotype
- Salmon choosing library type
- Map gene list to pathway and visualize it
- KEGG pathway per genes relation
- Enrichment analysis for custom set
- GDC data only cancer sample without normal sample
- Getting interesting gene ontology analysis result
- Interpretation of DE gene and mutation in normal/cancer sample
- Sample clustering from TCGA dataset
- Filtering the result of transcription factor binding matrix prediction from PWM with FIMO software
- Tools to analyze protein sequence if mutation occur
- miRNA binding detection from RNA-seq reads
- PPM, PSSM, and PWM
- Ensembl regulatory build promoter region and gene name
- Workshop or training related to Bioinformatics
- Is there any paper about motif finding based on PWM on genome sequence?
- Download transfac public database
- Ensembl chromosome other than 1-22, X, and Y
- Transcription factor binding site prediction program/algorithm
- Cytoscape 3.3.0 visualize network with up/down regulated color
- Biological difference for selecting alignment reference to DNA vs cDNA
- miRNA binding position in gene transcript (alignment of cDNA FASTA and miRNA FASTA file)
- Get sequence from aligned BAM file according to interval in BED file
- Get miRNA expression from RNA-seq
- Alternative sequence gene Ensembl ID
- KEGG pathway gene list different from the picture
- Microarray and RNA-seq different result
- About logFC and p-value( and adj p-value)
- Comparison of microarray and RNA-seq data
- Data with only 1 pair for DEG analysis
- Salmon warning detected suspicious pair
- About Gene Transcriptional Regulatory Network
- Varscan2 warning : resetting normal
- DGE analysis suggestion : linearity between TF and target gene expression level
- Gene name to Ensembl ID
- Get accumulated gene expression from alternative splicing in DESeq2
- Detect variation in promoter region from Exome-seq and RNA-seq
- Processng cuffnorm output
- From cuffnorm to DESeq
- Gene expression level with RNA-seq
- BSSeq alignment algorithm/software
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Pierre Lindenbaum
