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Problem with readFast5Summary in IONiseR related to HDF5
ioniser bioinformatics minion
updated 6.6 years ago by ▴ 380 • written 7.1 years ago by • 0
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3
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Gene Ontology and Gene Set Enrichment
rna-seq bioinformatics gene ontology gene set enrichment go
updated 7.6 years ago by ★ 1.2k • written 7.6 years ago by ▴ 10
2
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5
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1.5k
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Differential Gene Expression
deseq2 bioinformatics rna-seq Tutorial
updated 7.6 years ago by 41k • written 7.6 years ago by ▴ 10
3
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6
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1.9k
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Analyzing Open source PPI databases
ppi bioinformatics
updated 8.7 years ago by 25k • written 8.7 years ago by ▴ 10
0
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2
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3.1k
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AffyMetrix CEL file; data is already transformed too log2
affy microarray bioinformatics
9.2 years ago kanacska ▴ 10
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2
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2.4k
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Job: Bioinformatics Research Associate, University of Adelaide
job Job australia bioinformatician job bioinformatics
written 8.8 years ago by ▴ 170
3
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7
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2.5k
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How to convert bia file to tsv file
samtools bioinformatics
8.9 years ago engr.yahya602 • 0
3
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6
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1.9k
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Regressing effect of treatment on RNA-seq expected count from rsem.
RNA rna-seq science bioinformatics
updated 7.0 years ago by 65k • written 7.0 years ago by ▴ 20
0
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1
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In DESeq2, why LRT result's LFC doesn't match with any of Wald test result's LFC?
deseq2 bioinformatics
updated 7.5 years ago by 41k • written 7.5 years ago by • 0
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Job: Postdoctoral Research Fellow in Bioinformatics – Systems Biology of Childhood Cancer
bioinformatics systemsbiology cancer job austria Job
8.8 years ago • updated 8.7 years ago heinrich.kovar ▴ 10
1
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2
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topGO for Gene Ontology and Gene Set enrichment
topgo gene ontology gene set enrichment rna-seq bioinformatics
updated 7.3 years ago by ▴ 730 • written 7.6 years ago by ▴ 10
4
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2
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1.2k
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seeking a paper or journal review about repeated multiple testing for Biological ChIP-seq replicates?
bioinformatics paper multiple treatments biologicalreplicates
updated 7.8 years ago by 50k • written 7.8 years ago by ▴ 80
1
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1
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5.5k
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Mfuzz: fill.NA - Warning messages: argument is not numeric or logical: returning NA
mfuzz clustering bioinformatics proteomics timecourse
updated 8.2 years ago by 1.6k • written 8.2 years ago by • 0
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News: New Master of Science in Quantitative and Computational Biology at University of Trento, Italy
computational biology bioinformatics teaching master News
updated 7.8 years ago by • 0 • written 7.9 years ago by ▴ 10
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1.4k
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How do i perform chi square test in r?
microarray chisquare bioconductor bioinformatics
updated 8.5 years ago by ★ 28k • written 8.5 years ago by ▴ 10
0
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2
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733
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abs() error in rstudio
Bioconductor BiocManager abs() Bioinformatics
written 16 months ago by • 0
1
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2
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947
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Results Goana after edgeR pipeline
EdgeR Bioinformatics Goana
2.7 years ago Barista • 0
1
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5
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3.2k
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How to convert a bam file into tsv file format?
bioinformatics
updated 8.6 years ago by 50k • written 8.6 years ago by • 0
1
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2
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1.3k
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Not many DE genes using glmTreat
EdgeR Bioinformatics Transcriptomics Quantseq
2.7 years ago Barista • 0
2
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2
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1.2k
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How to deal with Expression set assembly problem?
deconvolution r scRNAseq bioinformatics
2.2 years ago Hasan Alanya • 0
2
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2
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962
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Help for Research Proposal
drug development pathways bioinformatics
updated 5.4 years ago by ★ 13k • written 5.4 years ago by • 0
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1
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News: Exploiting computational immunology to understand the immune system| Symposium
computational biology immunology bioinformatics symposium RIMLS News
updated 7.3 years ago by • 0 • written 7.4 years ago by • 0
1
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6
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2.7k
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DESeq2 unbalanced sample size
deseq2 bioconductor bioinformatics statistics
updated 14 months ago by 41k • written 5.4 years ago by • 0
0
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1
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1.6k
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Get Gene IDs for a list of Gene Names in R
r bioinformatics org.Hs.eg.db genetics
updated 5.8 years ago by 25k • written 5.8 years ago by • 0
0
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2
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2.5k
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Error in CummeRbund installation
cummerbund rnaseq bioinformatics bioconductor R
updated 8.9 years ago by 65k • written 8.9 years ago by • 0
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1
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1.2k
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surrogate variable analysis using R package "sva"
sva r bioinformatics
updated 7.6 years ago by ▴ 760 • written 7.6 years ago by ▴ 10
3
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4
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973
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edgeR analysis of cells treated with either drug1, drug2, or a time matched control at two different time points, did I set this up correctly?
edger rnaseq gene expression bioinformatics
updated 5.6 years ago by 50k • written 5.6 years ago by • 0
0
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2
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5.1k
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Converting Fastq to Fasta in R
R Bioinformatics Fastq Fasta
updated 5.3 years ago by 65k • written 5.3 years ago by • 0
1
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1
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1.2k
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FPKM normalization questions!
r fpkm bioinformatics
updated 7.5 years ago by ★ 28k • written 7.5 years ago by ▴ 10
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0
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1.4k
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Job: Senior Postdoctoral Fellow in Computational Biology/Bioinformatics : Adelaide, Australia
postdoc bioinformatics network analysis australia systemsbiology Job
8.0 years ago david.lynn • 0
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0
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Job: Computational Biologist (Genome Statistical Analyst) position in CRUK Manchester Institute, UK
job bioinformatics ngs genomics statistics Job
8.2 years ago Hui Sun Leong ▴ 10
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2.1k
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Job: PhD Positions in Helsinki
bioinformatics job Helsinki Finland Job
8.2 years ago Simon Anders ★ 3.7k
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2.4k
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Job: Full position as Bioinformatician at ETH Zurich in Personalized Medicine Data Fusion and Method Implementation
bioinformatics personalized medicine genomics Job
9.5 years ago Daniel Stekhoven ▴ 10
0
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3
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1.5k
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How to extract / pull out each row(a.k.a, single genome interval ) from given bed files by row by row for meta analysis?
r bioinformatics peakset
updated 12 months ago by • 0 • written 8.3 years ago by ▴ 80
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0
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Job: Postdocs and PhD students in the areas of Bioinformatics, Biostatistics or Medical Informatics
jobs job bioinformatics R Job
8.4 years ago Frank Kramer ▴ 60
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Job: Post-doc Position in Epigenetic Bioinformatics
cancer sequencing epigenetics computational biology bioinformatics Job
8.4 years ago Yassen Assenov ▴ 10
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Job: Data Scientist, Mount Sinai School of Medicine, New York, NY USA
job postdoctoral fellow computational biology bioinformatics new york Job
7.4 years ago supindab ▴ 10
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1.6k
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Job: Bioinformatics Post-Doc Positions
cancer BIOINFORMATICS genomics RNAseq miRseq Job
9.2 years ago aaron • 0
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Job: Faculty Position in Computational Systems Biology at UC Riverside
systemsbiology bioinformatics position Job
9.5 years ago Thomas Girke ★ 1.7k
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Job: Bioinformatician - The Ragon Institute of MGH, MIT and Harvard
bioinformatician job bioinformatics immunology HIV Job
7.4 years ago • updated 7.1 years ago Ragon Institute of MGH, MIT and Harvard • 0
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Job: Job Opening: Computational Biologists in Cambridge, MA and NYC
ngs computational biology R genomics bioinformatics Job
8.5 years ago mmartin ▴ 20
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1.2k
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Job: Bioinformatician/Bioinformatics position, IMB Mainz, Germany
bioinformatics germany job Job
7.5 years ago sergisayolspuig ▴ 80
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Job: Job: Senior Scientist, Oncology Translational Research Johnson and Johnson
cancer jobs computational biology bioinformatics Job
5.9 years ago Michael Gormley ▴ 60
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Job: PhD Studentship: Genome-scale analysis of host-pathogen interactions
rnaseq single cell bioinformatics R epigenomics Job
8.5 years ago Garry Myers • 0
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Job: Chief Data Scientist
bioinformatics Job
7.5 years ago kaufmanm ▴ 10
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Job: PhD Position in Bioinformatics
bioinformatics protein variantannotation data integration Job
7.4 years ago stephan.pabinger • 0
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Job: Postdoc Positions in Computational Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
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7.5 years ago cristina della beffa ▴ 30
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Job: Multiple postdoctoral fellowships are available immediately in the Gehlenborg Lab in the Department of Biomedical Informatics at Harvard Medical Scho…
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8.5 years ago Doe, Aimee ▴ 40
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Job: FIMM-EMBL International PhD program now accepting applications
bioinformatics molecular medicine PhD Job
7.3 years ago gretchen.repasky ▴ 20
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Job: Harvard Medical School - Research Fellow Position at the Department of Biomedical Informatics
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8.5 years ago Doe, Aimee ▴ 40
50 results • Page 1 of 1
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Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by James W. MacDonald 65k
You will need to show some reproducible code for anybody to track this down. Please note that `DESeq2` has been used by thousands of people…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
My code for the sessionInfo() . If the pictures are too big, I will downsize them. THank you again for reading my post ! ```r > sessionInf…
Comment: Reproducibility issue with scran together with lapply and BiocParallel by ATpoint ★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Votes
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
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