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349 results • Page
1 of 7
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Views
Votes
Replies
269
votes
39
replies
148k
views
29 follow
Tutorial:
How to download raw sequence data from GEO/SRA
fastq
SRA
download
GEO
bam
updated 22 days ago by
Ram
36k • written 7.7 years ago by
Obi Griffith
19k
262
votes
33
replies
81k
views
24 follow
Tutorial:
Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates
tutorial
Tutorial
updated 3 months ago by
tshtatland
▴ 90 • written 8.6 years ago by
Obi Griffith
19k
233
votes
176
replies
77k
views
73 follow
Tutorial:
Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq
TCGA
Survival
Tutorial
updated 9 weeks ago by
Ram
36k • written 6.8 years ago by
TriS
★ 4.5k
192
votes
47
replies
65k
views
33 follow
Tutorial:
Analysing Microarray Data In Bioconductor
tutorial
bioconductor
microarray
analysis
tutorial
Tutorial
updated 3 months ago by
javanokendo
• 0 • written 9.6 years ago by
Obi Griffith
19k
147
votes
35
replies
55k
views
33 follow
Tutorial:
Tools For Metagenomic Data Analysis
metagenomics
Tutorial
next-gen
updated 12 days ago by
Bramadi Arya
• 0 • written 9.5 years ago by
vijay
★ 1.6k
142
votes
34
replies
49k
views
17 follow
Tutorial:
Working with MAF files (Mutation Annotation Format) from the TCGA (The Cancer Genome Atlas)
mutation
maf
tcga
cancer
music
Tutorial
updated 9 days ago by
Ram
36k • written 9.1 years ago by
Cyriac Kandoth
5.8k
141
votes
21
replies
28k
views
12 follow
Tutorial:
A few words for R beginners
Swirl
R
updated 16 days ago by
Ram
36k • written 7.4 years ago by
Parham
★ 1.6k
139
votes
67
replies
38k
views
17 follow
Tutorial:
Network plot from expression data in R using igraph
R
Tutorial
microarray
RNA-Seq
network
updated 7 months ago by
Hamtaro
▴ 10 • written 4.5 years ago by
Kevin Blighe
81k
128
votes
25
replies
68k
views
14 follow
Tutorial:
Piping With Samtools, Bwa And Bedtools
unix
samtools
bwa
bedtools
updated 6 weeks ago by
Ram
36k • written 10.1 years ago by
Ying W
★ 4.1k
122
votes
119
replies
22k
views
22 follow
Tutorial:
Survival analysis with gene expression
survival analysis
cox
geo
gene expression
Tutorial
10 days ago by
Kevin Blighe
81k
113
votes
66
replies
34k
views
20 follow
Tutorial:
[Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera
fastq-dump
ENA
Fastq
Tutorial
10 months ago by
ATpoint
60k
99
votes
8
replies
25k
views
8 follow
Tutorial:
Guide to TCGA data
TCGA
cancer
tools
RNA-Seq
clinical
Tutorial
updated 5.5 years ago by
ewre
▴ 250 • written 6.2 years ago by
Jordan Anaya
★ 1.1k
98
votes
16
replies
27k
views
18 follow
Tutorial:
Heatmaps in R
Tutorial
R
heatmap
16 days ago by
Jean-Karim Heriche
25k
94
votes
25
replies
30k
views
11 follow
Tutorial:
Fastq Quality Control Shootout
quality
fastq
trimming
qc
tutorial
Tutorial
updated 10 weeks ago by
Ram
36k • written 9.7 years ago by
Istvan Albert
93k
91
votes
6
replies
19k
views
6 follow
Tutorial:
Creating workflows with snakemake and conda
snakemake
conda
workflow
Tutorial
updated 18 months ago by
psschlogl
▴ 30 • written 3.7 years ago by
finswimmer
15k
86
votes
19
replies
29k
views
12 follow
Tutorial:
Machine Learning For Cancer Classification - Part 1 - Preparing The Data Sets
classification
microarray
expression
bioconductor
Tutorial
updated 5.4 years ago by
yuanjun.ma
• 0 • written 8.6 years ago by
Obi Griffith
19k
85
votes
95
replies
27k
views
23 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
Tutorial
1000
genomes
PCA
PLINK
updated 11 days ago by
dongxinyu510
• 0 • written 3.7 years ago by
Kevin Blighe
81k
81
votes
8
replies
7.4k
views
6 follow
Tutorial:
Current Topics in Genome Analysis 2014 (collection of educational lectures)
genomics
workshop
Tutorial
lectures
training
updated 11 days ago by
Ram
36k • written 7.9 years ago by
Malachi Griffith
19k
81
votes
27
replies
25k
views
18 follow
Tutorial:
How to create a mutation landscape (waterfall) plot with GenVisR
GenVisR
BioConductor
R
Graphics
Tutorial
updated 5 months ago by
isd1989
• 0 • written 6.2 years ago by
Obi Griffith
19k
76
votes
13
replies
13k
views
12 follow
Tutorial:
Exploring cancer mutation data portals
TCGA
Cancer
ICGC
Data-Portal
Mutation
updated 7 months ago by
Ram
36k • written 8.0 years ago by
Malachi Griffith
19k
76
votes
32
replies
13k
views
17 follow
Tutorial:
Enrichment Analysis, Clustering and Scoring with pathfindR
R
pathway
enrichment
active subnetwork
Tutorial
updated 14 months ago by
VolEr
▴ 30 • written 3.9 years ago by
egeulgen
★ 1.2k
75
votes
40
replies
25k
views
23 follow
Tutorial:
Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm
rna-seq
bioconductor
updated 11 weeks ago by
Ram
36k • written 8.6 years ago by
Irsan
★ 7.5k
75
votes
1
reply
49k
views
Tutorial:
How To Ask Good Questions On Technical And Scientific Forums
tutorial
Tutorial
written 8.9 years ago by
Eric Normandeau
11k
75
votes
70
replies
14k
views
18 follow
Tutorial:
Clustering of DAVID gene enrichment results from gene expression studies
enrichment
Tutorial
david
updated 3 months ago by
Kristy
• 0 • written 4.3 years ago by
Kevin Blighe
81k
72
votes
13
replies
64k
views
10 follow
Tutorial:
Machine Learning For Prediction of Relapse in Cancer - Part 2 - Building A Random Forest Classifier
r
cancer
classification
tutorial
Tutorial
updated 3.7 years ago by
Ram
36k • written 8.5 years ago by
Nicholas Spies
★ 1.2k
72
votes
59
replies
20k
views
15 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
1000 genomes
PCA
VCF
PLINK
Tutorial
updated 7 months ago by
sara27888
• 0 • written 4.7 years ago by
Kevin Blighe
81k
72
votes
48
replies
14k
views
15 follow
Tutorial:
For Short Reads, Which Aligners Find All Hits Given Certain Edit Distance Threshold?
bwa
alignment
ngs
tutorial
Tutorial
updated 6 weeks ago by
Ram
36k • written 9.3 years ago by
lh3
33k
70
votes
5
replies
9.8k
views
8 follow
Tutorial:
Bioinformatics For Metagenomic Analyses
QC
taxonomy
metagenomics
updated 6 weeks ago by
Ram
36k • written 8.1 years ago by
umer.zeeshan.ijaz
★ 1.8k
69
votes
3
replies
31k
views
Tutorial:
Revisiting the FastQC read duplication report
fastqc
updated 6 months ago by
Ram
36k • written 7.8 years ago by
Istvan Albert
93k
69
votes
19
replies
8.7k
views
15 follow
Tutorial:
Gene Set Enrichment Analysis
enrichment
microarray
Tutorial
GSEA
RNA-Seq
25 days ago by
Hamid Ghaedi
★ 2.5k
69
votes
16
replies
56k
views
10 follow
Tutorial:
How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
samtools
bcftools
htslib
Tutorial
updated 5 months ago by
jwalewski
• 0 • written 3.8 years ago by
otwtgin2010
▴ 460
68
votes
14
replies
12k
views
15 follow
Tutorial:
List Of Bioinformatics Books
bioinformatics
tutorial
books
Tutorial
updated 12 weeks ago by
Paul A. Gagniuc
▴ 40 • written 9.0 years ago by
Medhat
9.3k
67
votes
6
replies
23k
views
7 follow
Tutorial:
Rna-Seq Review Papers
papers
rna-seq
tutorial
Tutorial
updated 6.3 years ago by
Art_SG
• 0 • written 9.7 years ago by
Istvan Albert
93k
66
votes
9
replies
46k
views
7 follow
Tutorial:
Reference Assembly - Mapping Reads To A Reference Genome
mapping
samtools
bwa
reference
Tutorial
updated 8 months ago by
Ram
36k • written 8.9 years ago by
Joseph Hughes
★ 2.9k
63
votes
5
replies
6.3k
views
10 follow
Tutorial:
Informatics of RNA-Seq.
RNA-Seq
next-gen
Tutorial
updated 6.5 years ago by
Malachi Griffith
19k • written 6.8 years ago by
GouthamAtla
11k
63
votes
26
replies
9.7k
views
7 follow
Tutorial:
Parallel processing in R
R
Tutorial
biocparallel
mclapply
foreach
2.5 years ago by
Kevin Blighe
81k
63
votes
25
replies
22k
views
14 follow
Tutorial:
How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
rna-seq
tutorial
Tutorial
updated 2.0 years ago by
Ram
36k • written 8.3 years ago by
Istvan Albert
93k
63
votes
13
replies
12k
views
11 follow
Tutorial:
Tutorial (How to analyze) on Whole Exome sequencing. Common Errors. Best Practices.
muTect
GATK
Picard
Exome
updated 3 months ago by
Ram
36k • written 7.5 years ago by
Chirag Nepal
★ 2.3k
61
votes
26
replies
8.1k
views
11 follow
Tutorial:
Generating consensus sequence from bam file
bam
consensus
fasta
Tutorial
updated 11 months ago by
bioinfo8
▴ 180 • written 3.2 years ago by
finswimmer
15k
60
votes
2
replies
6.6k
views
Tutorial:
Table Of Contents To All Review Paper Compilations On Biostar
Tutorial
papers
updated 8 months ago by
Ram
36k • written 9.7 years ago by
Istvan Albert
93k
60
votes
49
replies
36k
views
22 follow
Tutorial:
Creating Interactive Volcano Plots with R and Plot.ly
R
plotly
volcano plot
Tutorial
updated 12 months ago by
Ram
36k • written 5.6 years ago by
steve
★ 3.1k
60
votes
6
replies
8.5k
views
Tutorial:
Minimum Standards For Bioinformatics Command Line Tools
command-line
tools
bioinformatics
Tutorial
3.4 years ago by
Medhat
9.3k
57
votes
15
replies
9.6k
views
Tutorial:
Which human reference genome should I use?
genome
alignment
assembly
Tutorial
3.5 years ago by
finswimmer
15k
57
votes
25
replies
34k
views
15 follow
Tutorial:
Protocol To Downlad TCGA Data From GDC
GDC
TCGA
Download
methylation
Tutorial
updated 3.5 years ago by
ATpoint
60k • written 5.8 years ago by
Shicheng Guo
★ 9.0k
55
votes
41
replies
16k
views
16 follow
Tutorial:
Polish PacBio assembly with latest PacBio tools : an affordable solution for everyone
arrow
pbalign
pacbio
polishing
smrt limk
Tutorial
updated 2.0 years ago by
zjl1983
• 0 • written 4.7 years ago by
Rox
★ 1.4k
52
votes
5
replies
13k
views
6 follow
Tutorial:
Machine Learning For Cancer Classification - Part 4 - Plotting A Kaplan-Meier Curve For Survival Analysis
r
tutorial
Tutorial
updated 4.9 years ago by
jmzeng1314
▴ 130 • written 8.5 years ago by
Nicholas Spies
★ 1.2k
51
votes
19
replies
40k
views
6 follow
Tutorial:
Visualizing Chip-Seq Data Using Ucsc [Bigwig]
chip-seq
rna-seq
bigwig
visualization
ucsc
tutorial
Tutorial
updated 6.3 years ago by
Shicheng Guo
★ 9.0k • written 10.1 years ago by
Sukhi Singh
10k
51
votes
3
replies
21k
views
Tutorial:
Sam File Format - Lesser Known Tips And Tricks
sam
format
tutorial
Tutorial
updated 9.3 years ago by
Ying W
★ 4.1k • written 9.4 years ago by
Ya
▴ 300
49
votes
3
replies
3.5k
views
Tutorial:
[[ Please read before posting a question ::: How To Ask A Good Question ]]
tutorial
Tutorial
how-to
2.3 years ago by
ATpoint
60k
48
votes
7
replies
10k
views
7 follow
Tutorial:
Genome Assembly Review Papers
papers
assembly
tutorial
Tutorial
updated 9.3 years ago by
lh3
33k • written 9.7 years ago by
Istvan Albert
93k
349 results • Page
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Recent Votes
A: Is it possible to run haplotypecaller in gnu parallel ?
Is it possible to run haplotypecaller in gnu parallel ?
A: Identifying De Novo Mutations from vcf files
Answer: Lasso regression and cross-validation on RNA seq dataset
A: How to combine multiple pheatmap figures and use common legend?
Comment: Help with kallisto-bustools: how to interpret the inspect.json output file
Answer: SARS-CoV-2 lineages complete reference genomes
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Answer: Lasso regression and cross-validation on RNA seq dataset
by
Mensur Dlakic
★ 18k
It is not clear whether you have 192 datasets or 192 features in some undefined number of datasets, but either way cross validation is a sm…
Comment: SARS-CoV-2 lineages complete reference genomes
by
GenoMax
115k
I don't know if the following two resources are going to provide `reference` genomes. You may have to go to GSAID for that.
Answer: SARS-CoV-2 lineages complete reference genomes
by
GenoMax
115k
From EBI: https://www.covid19dataportal.org/sequences?crossReferencesOption=all ![EBI][1] [1]: /media/images/04dd9b11-77a8-4327-8…
Answer: Software to draw protein domains of proteins
by
cmdcolin
★ 2.1k
tools mentioned by other users are great, a couple more tools here https://cmdcolin.github.io/awesome-genome-visualization/?latest=true&tag…
Answer: SARS-CoV-2 lineages complete reference genomes
by
GenoMax
115k
At [**NCBI SARS-CoV-2**][1] resource page. Be sure to switch to `Nucleotide` tab and then click on pango lineage search. ![Pango][2] …
Answer: comparisons between 2 ChIP-seq datasets
by
jared.andrews07
★ 13k
Honestly, I'd just eyeball the tracks in IGV. It's usually pretty apparent. If you want more objective measures, you could look at total…
Comment: data correaltion
by
Jeremy
▴ 130
FYI the cor.test() function will display a p-value in addition to the correlation coefficient.
Comment: Inflation in Imputed data
by
desicasares@gmail.com
▴ 10
Thank you for your answer...the populations I am using are Spanish, North European and Italian individuals. In the case of the Italians t…
Comment: MAF in R
by
malgorzata.sobczak07
• 0
You're the best! Thanks! :)
Comment: Help with kallisto-bustools: how to interpret the inspect.json output file
by
dsull
★ 3.0k
Correct, which is why you should load your output into R or python and filter your cells (i.e. do the "knee plot"). See the kallisto | bust…
Answer: MAF in R
by
Ram
36k
You can use `HardyWeinberg::maf` to calculate MAF from a vector of frequencies. You can create this vector of HOM/HET/HOM-ALT frequencies u…
Comment: MAF in R
by
malgorzata.sobczak07
• 0
Yeah, sorry :)
Comment: MAF in R
by
Ram
36k
Your code won't work. You'll need to quote the allele strings
Comment: The minor allele frequency
by
Negatyvna
• 0
Yes, I would like to do the second option
Comment: NCBI tblastx remote
by
ailton
• 0
Thanks a lot for the help. I managed to run it using its parameters, I also used other methods to run tblasx **$ tblastx -db databases/refe…
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