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Showing top results for tag: cancer • reset
1
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2
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170
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Variant Allele Frequency
Cancer
updated 8 days ago by ★ 2.4k • written 8 days ago by • 0
0
votes
0
replies
75
views
Weird PCA plot using WGCNA results
cancer PCA expression WGCNA plot
7 days ago by seta ★ 1.5k
0
votes
0
replies
144
views
Job: PhD student for a computational breast cancer research project
Bioinformatics PhD Cancer Omics
9 days ago by s.vosberg • 0
3
votes
3
replies
165
views
Germline Cancer Mutations
Cancer
updated 9 days ago by ★ 2.5k • written 9 days ago by • 0
1
vote
2
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215
views
Module preservation analysis using WGCNA
cancer expression WGCNA samples gene
updated 12 days ago by ★ 1.7k • written 14 days ago by ★ 1.5k
0
votes
1
reply
133
views
Approach to building regression models or classifiers with high number of parameters but small sample size
cancer machine-learning R scRNA-seq RNA-seq
updated 22 days ago by ★ 13k • written 22 days ago by ▴ 10
0
votes
1
reply
136
views
Dataset of different timepoints of a cancers progression in the same patient?
cancer RNAseq
updated 24 days ago by ▴ 180 • written 24 days ago by • 0
3
votes
5
replies
275
views
Downloading WGBS sequencing reads for cancer sample and healthy sample
Dataset Cancer WGBS Healthy
5 days ago by Nishat • 0
0
votes
0
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133
views
Job: PDRA in Computational Biophysics and Cancer Research, University of Manchester, UK
Bioinformatics StructuralGenomics Cancer pH-dependence
5 weeks ago by jim.warwicker • 0
0
votes
0
replies
145
views
Job: Post-doctoral Fellow in Cancer Biology and Immunology
biology immunology Cancer molecular
7 weeks ago by waihungh ▴ 20
0
votes
0
replies
167
views
Job: Postdoctoral Fellowship in Bioinformatics and Liver Cancer Genomics
biopsy NGS genomics Liquid Cancer Bioinformatics sequencing Single-cell
7 weeks ago by waihungh ▴ 20
0
votes
0
replies
224
views
Job: PhD Scholarship in Bioinformatics and Liver Cancer Genomics
biopsy NGS genomics Liquid Cancer Bioinformatics sequencing Single-cell
7 weeks ago by waihungh ▴ 20
0
votes
3
replies
207
views
Annotate variants for cancer genomics studies
oncology cancer genomics variant
updated 9 weeks ago by ▴ 560 • written 10 weeks ago by ▴ 490
3
votes
2
replies
276
views
Suggestions for an undergraduate research project on glioblastoma
glioblastoma Python Cancer R
updated 9 weeks ago by 34k • written 10 weeks ago by ▴ 90
4
votes
3
replies
248
views
which genes causes breast cancer?
Breast Cancer
updated 3 months ago by 49k • written 3 months ago by • 0
0
votes
3
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326
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Identifying samples from COSMIC/cBioportal etc with only a specific driver mutation
cancer genomics
updated 12 weeks ago by 34k • written 3 months ago by • 0
7
votes
3
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441
views
How to make a summary plot like below?
cancer classes Oncoplots
updated 3 months ago by ▴ 200 • written 3 months ago by • 0
0
votes
0
replies
122
views
How to merge the mutations from multiple samples of one patient
MutSig2CV_NC MutSig2CV cancer mutation merge
3 months ago by Rongxin ▴ 30
22
votes
1
reply
4.0k
views
Tutorial: Methylation Analysis Tutorial in R_part1
Tutorial cancer methylation R
updated 3 months ago by ▴ 30 • written 11 months ago by ★ 1.7k
0
votes
0
replies
227
views
Tool: Help solve the cancer puzzle & benefit your research! SimBioSys PhenoScope for integrative multi-modal and multi-omic data analytics
multi-modal multi-omic breast analytics cancer imaging
3 months ago by johnpfeiffer • 0
0
votes
1
reply
210
views
Important genes beyond PAM50 for breast cancer classification
genes cancer deeplearning classification pam50
3 months ago by udi • 0
0
votes
0
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168
views
Tool: SimBioSys PhenoScope - a cloud-based multi-modal multi-omic data analytics platform for oncology researchers
cloud-based analytic cancer multi-modal multi-omic
3 months ago by johnpfeiffer • 0
0
votes
0
replies
173
views
Job: Senior Staff Bioinformatician at the University of Melbourne Centre for Cancer Research
cancer genomics
4 months ago by Oliver • 0
1
vote
0
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243
views
Job: Computational Biology Lab Head, Brain Cancer Centre, Melbourne, Australia
cancer wehi australia
4 months ago by Gordon Smyth ★ 3.3k
3
votes
2
replies
351
views
Is anticancer action of HDAC inhibitors - cancer cells specific or it may cause death to other cell types ?
cancer
updated 5 months ago by 25k • written 5 months ago by ▴ 20
0
votes
0
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267
views
Job: Group Leader Computational Cancer Biology - VIB-KU Leuven, Belgium
vib groupleader cancer biology computational
5 months ago by leen.notebaert • 0
3
votes
2
replies
378
views
Contradiction in Harzard ratio and Log fold change
Foldchange Cancer HR HarzardRatio LogFC
5 months ago by Amir.Asgary ▴ 30
0
votes
4
replies
440
views
How to plot a image like this.
Genome R plot Cancer
updated 12 weeks ago by 34k • written 5 months ago by ▴ 10
0
votes
1
reply
592
views
Where to download raw counts (RNAseq) and breakpoints coordinates (cancer related) for testing?
cancer rawcounts(RNAseq) breakpoint downloaddata
updated 5 months ago by 77k • written 5 months ago by ★ 1.1k
1
vote
2
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1.2k
views
Interpretation of functional prediction pathogenicity scores regarding variants with multiple transcripts in ANNOVAR
annovar pathogenicity cancer CADD
5 months ago by svlachavas ▴ 750
0
votes
0
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220
views
Job: Postdoc in computational cancer biology at IEO, Milan, Italy
ppi cancer networks genomics
5 months ago by martin.schaefer ▴ 10
0
votes
0
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298
views
Job: Cancer Bioinformatician @ University of East Anglia - Norwich Medical School UK
uk cancer postdoc
5 months ago by dan.brewer ▴ 120
4
votes
2
replies
623
views
Extracting specific cancer types from MAF (Mutation Annotation Format) files from TCGA(The Cancer Genome Atlas)
ENCODE mutation maf TCGA cancer
5 months ago by peter ▴ 10
14
votes
10
replies
5.2k
views
Tool: Arriba: Fast and accurate gene fusion detection from RNA-Seq data
RNA-Seq cancer variant calling gene fusion Tool
6 months ago by uhrigs ▴ 140
0
votes
0
replies
544
views
Job: PhD student in precision cancer bioinformatics | Charite, Berlin, Germany
cancer ngs berlin clinical precision Job
6 months ago by naveed.ishaque • 0
0
votes
0
replies
228
views
A database of cancer super-enhancers
ChIP-Seq super-enhancers cancer
6 months ago by MoHallal • 0
14
votes
2
replies
1.2k
views
Tutorial: Methylation Analysis Tutorial in R_part2
methylation RNA-Seq R cancer Tutorial
6 months ago by Hamid Ghaedi ★ 1.7k
0
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0
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165
views
Looking for VCF files and clinical data for cancer (prostate or cll or breast)
vcf cancer somatic mutations access to data
6 months ago by ansakim20 • 0
0
votes
0
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162
views
Finding mutational burden in TCGA dataset
genome python UTR tcga cancer
6 months ago by Jamie Watson • 0
0
votes
1
reply
215
views
METABRIC sample IDs
METABRIC sample cancer mRNA ID
updated 7 weeks ago by ★ 1.4k • written 7 months ago by • 0
2
votes
4
replies
222
views
where to find cancer data
SNP cancer next-gen data fastq
updated 7 months ago by 53k • written 7 months ago by • 0
2
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3
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465
views
VEP for cancer annotation using COSMIC
VEP COSMIC Cancer
updated 7 months ago by 22k • written 7 months ago by ▴ 40
0
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5
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332
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development of NGS pipeline for variant calling in lung cancer
cancer NGS pipeline snp next-gen
updated 7 months ago by ▴ 30 • written 7 months ago by • 0
0
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0
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220
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Calling UTRs in TCGA dataset
TCGA cancer UTR ORF
7 months ago by Jamie Watson • 0
6
votes
11
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5.8k
views
9 follow
RNAseq data and PAM50 method
rna-seq PAM50 Breast Cancer unsupervised
updated 8 months ago by 20 • written 7.3 years ago by ▴ 20
25
votes
23
replies
11k
views
14 follow
Anyone Has A Working Example On How To Run BROAD's ABSOLUTE On Exome Sequencing Data?
cancer exome-sequencing copynumber
updated 8 months ago by • 0 • written 7.6 years ago by ★ 3.0k
16
votes
2
replies
5.7k
views
Job: Open positions at the Center for Molecular Oncology, MSKCC, New York
python R cancer genetics sequencing Job
8 months ago by Cyriac Kandoth 5.7k
8
votes
4
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369
views
Pathway analysis of a list of possible cancer driver genes
pathway analysis cancer driver genes
updated 8 months ago by 77k • written 8 months ago by ▴ 210
0
votes
0
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287
views
Correcting variant allele fraction using tumor purity (experimentally measured)
variant calling sequencing cancer SNP next-gen
9 months ago by Luca Beltrame ▴ 220
0
votes
0
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575
views
Job: Senior Research Associate in Bioinformatics @ University of East Anglia - Norwich Medical School, UK
cancer bioinformatics postdoc biomarkers Job
9 months ago by dan.brewer ▴ 120
50 results • Page 1 of 1
Recent Votes
Question about ROH analysis by Plink 1.9
Comment: Flat Volcano plot
Answer: Is there any software that can use ATAC-seq to identify super enhancer
Comment: Genozip: A new compression tool for FASTQ, BAM, VCF and more
Comment: How to remove Illumina TruSeq Index adapters reverse (R2 reads )
How can I draw this plot?
Interpreting output of BCFtools RoH
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Recent Replies
Comment: PRS in UK Biobank - no covariate file and no phenotype file by agamemnon • 0
Thank you, I have the right target data and will also extract the phenotype and covariate data. While running the first script for QCing …
Comment: Question about ROH analysis by Plink 1.9 by gubrins ▴ 90
Heys, I'm struggling to having results from plink when I try to calculate the roh in my data. I did the snp calling both with gatk and with…
Comment: How to remove Illumina TruSeq Index adapters reverse (R2 reads ) by GenoMax 106k
Can you post an example of what you are referring to? Normally trimming programs should check reverse complements of sequences they are loo…
Comment: Genozip: A new compression tool for FASTQ, BAM, VCF and more by matthew.pobox ▴ 10
This seems like a great tool which has been seriously overlooked. I've been testing it out and was able to reproduce the compression ra…
Comment: get read length from sra by Renesh ★ 2.0k
The suggested methods works. Here is another method using the [SRA toolkit][1] fastq-dump -X 1 -Z SRR5790106 | sed -n '2p' | awk '{ pr…
Comment: Primers trimming from Illumina paired-end reads by BBDuk software by GenoMax 106k
Following should work. Give it a try and let me know. bbduk.sh -Xmx2g in1=test_R1.fq in2=test_R2.fq out1=R1_trim.fq out2=R2_trim.fq li…
Answer: Database for Enhancers with Coordinates by Papyrus ★ 1.3k
Also check [EnhancerAtlas][1], apart from coordinates it provides predictions for enhancer-gene target interactions, which may be useful. …
Comment: How can I draw this plot? by gubrins ▴ 90
Heys, did you manage to plot it?
Comment: get read length from sra by GenoMax 106k
You will only get average length of reads (which may or may not be very useful) using [Entrezdirect][1]. $ esearch -db sra -query "SRR…
Comment: Interpreting output of BCFtools RoH by gubrins ▴ 90
Heys, did you manage in interpreting and visualizing the output? I'm in the same situation...
Comment: which tool can I use to detect CNVs? by brunobsouzaa ▴ 560
`cnvkit` and `ExomeDepth` are great tools for that. Also, both are pretty straightforward to use.
Comment: rsem-calculate-expression with STAR takes forever but without error by Fleur • 0
Thanks both! I will try :) :)
Comment: rsem-calculate-expression with STAR takes forever but without error by Fleur • 0
Ah yes, sounds similar to tmux which is what I'm using. That also makes sure that the job keeps running when you close the terminal. Thanks…
Comment: which tool can I use to detect CNVs? by patelk26 ▴ 250
You could try CNVkit. You can create a reference copy number profile without normal samples.
Answer: Is there any software that can use ATAC-seq to identify super enhancer by jared.andrews07 ★ 11k
The original paper actually used a collection of TFs + Mediator. ROSE was not designed for H3K27ac use, though both the authors and others …
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