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191 results • Page
2 of 4
Sort: Views
Rank
Views
Votes
Replies
9
votes
2
replies
5.4k
views
Tutorial:
From Data import to Normalization in Microarray Analysis using in R (Part I)
gene
R
updated 11 months ago by
Ram
43k • written 7.8 years ago by
majuang66
▴ 140
9
votes
4
replies
5.2k
views
Tutorial:
Unsupervised clustering on gene expression data
gene-expression
clustering
RNA-seq
7 months ago by
Hamid Ghaedi
3.1k
6
votes
2
replies
4.9k
views
Tutorial:
Yes .. BBMap can do that! - Part III clumpify (mark (and dedupe) duplicates without alignment), mutate (create mutant genomes) and other miscellaneou…
bbmap
3 months ago by
GenoMax
140k
15
votes
3
replies
4.6k
views
Tutorial:
NCBI blast tutorial
ncbi
blast
updated 11 months ago by
Ram
43k • written 7.9 years ago by
Eric Normandeau
11k
3
votes
4
replies
4.4k
views
Tutorial:
gencore: a tool to reduce sequencing noises by generating consensus reads
consensus
OpenGene
sequencing-noise
updated 10 months ago by
Ram
43k • written 5.9 years ago by
chen
★ 2.5k
6
votes
2
replies
4.1k
views
Tutorial:
GATK method for filtering vcf lines using GT values at all or multisample level.
genome
vcf
genotype
variant-filtration
updated 10 months ago by
Ram
43k • written 6.8 years ago by
kirannbishwa01
★ 1.6k
9
votes
9
replies
4.1k
views
Tutorial:
Determine % of reference genome covered by aligned SAM/BAM
reference-coverage
ngs
updated 10 months ago by
Ram
43k • written 6.5 years ago by
Kevin Blighe
87k
20
votes
14
replies
3.9k
views
Tutorial:
Video-tutorials: How to get started using EaSeq for interactive ChIP-seq data visualization and exploration (Windows)
ChIP-Seq
visualization
Windows
EaSeq
updated 11 months ago by
Ram
43k • written 7.9 years ago by
Mads Lerdrup
▴ 460
6
votes
2
replies
3.8k
views
Tutorial:
How to extract fastq files from SRA data that contains both paired and unpaired reads
fastq-dump
sra
updated 11 months ago by
Ram
43k • written 8.0 years ago by
thomaskuilman
▴ 840
3
votes
2
replies
3.8k
views
Tutorial:
Galaxy Tutorial on ChIP-seq
galaxy
ChIP-Seq
updated 10 months ago by
Ram
43k • written 6.9 years ago by
anton
▴ 30
10
votes
4
replies
3.8k
views
Tutorial:
CorLevelPlot - Visualise correlation results, e.g., clinical parameter correlations
correlation
corlevelplot
updated 10 months ago by
Ram
43k • written 6.1 years ago by
Kevin Blighe
87k
3
votes
1
reply
3.7k
views
Tutorial:
Importance of Array Quality Control - arrayQualityMetrics (PART I)
gene
R
updated 11 months ago by
Ram
43k • written 7.7 years ago by
majuang66
▴ 140
10
votes
2
replies
3.7k
views
Tutorial:
Graph visualization with igraph in R
Visualization
igraph
Graph
R
Network
updated 10 months ago by
Ram
43k • written 6.9 years ago by
Jean-Karim Heriche
27k
0
votes
0
replies
3.6k
views
Tutorial:
Park Test for Heteroskedasticity In R Commander
R
Park-Test
updated 10 months ago by
Ram
43k • written 6.2 years ago by
helgasaraswati
▴ 10
3
votes
4
replies
3.6k
views
Tutorial:
Gene Set Enrichment Analysis on T-BioInfo
gene
RNA-Seq
updated 9 months ago by
Ram
43k • written 5.4 years ago by
elia.brodsky
▴ 340
0
votes
0
replies
3.6k
views
Tutorial:
SFA (Stochastic Frontier Analysis) STATA 14
R
updated 10 months ago by
Ram
43k • written 6.1 years ago by
helgasaraswati
▴ 10
1
vote
4
replies
3.4k
views
Tutorial:
How to install C++ compilers/make from GNU for Gromacs?
Gromacs
Cpp-compilers
GNU
updated 11 months ago by
Ram
43k • written 7.8 years ago by
Hassan Rasouli
▴ 10
19
votes
2
replies
3.3k
views
Tutorial:
Beginner's Handbook to Next Generation Sequencing
NGS
updated 10 months ago by
Ram
43k • written 6.9 years ago by
support
▴ 640
1
vote
4
replies
3.3k
views
Tutorial:
Applying machine learning to NGS transcriptomic data
next-gen
RNA-Seq
updated 10 months ago by
Ram
43k • written 5.9 years ago by
elia.brodsky
▴ 340
3
votes
1
reply
3.2k
views
Tutorial:
Affymetrix HTA 2.0 id conversion
biomart
HTA
affymetrix
Affymetrix
2.0
updated 5 weeks ago by
MaxF
▴ 120 • written 2.6 years ago by
Kevin Blighe
87k
2
votes
0
replies
3.2k
views
Tutorial:
use the tool slicer to split big files (like FASTQ) to smaller files for parallel processing
opengene
slicer
fastq
splitter
updated 9 months ago by
Ram
43k • written 6.4 years ago by
chen
★ 2.5k
1
vote
3
replies
3.2k
views
Tutorial:
resolving error of sspace_standard
software-error
Assembly
updated 11 months ago by
Ram
43k • written 7.6 years ago by
reza
▴ 300
15
votes
1
reply
3.1k
views
Tutorial:
Current Topics in Genome Analysis 2016 (collection of educational lectures)
genomics
training
lectures
workshop
updated 11 months ago by
Ram
43k • written 7.9 years ago by
Malachi Griffith
19k
0
votes
1
reply
3.1k
views
Tutorial:
Accessing sequences using batch entrez
genome
updated 10 months ago by
Ram
43k • written 6.4 years ago by
mawia.martha
• 0
2
votes
0
replies
3.1k
views
Tutorial:
How to read multiple matrices from GEO into R and make multiple Seurat objects and merge them into a single object.
unix
Seurat
single-cell
rstats
updated 8 months ago by
Ram
43k • written 8 months ago by
Ming Tommy Tang
★ 3.8k
2
votes
6
replies
3.1k
views
Tutorial:
Rembrandt Glioma Data Analysis (PART I) - Are Gender specific genes related to cancer ?
gene
R
Rembrandt
updated 11 months ago by
Ram
43k • written 7.7 years ago by
majuang66
▴ 140
0
votes
0
replies
3.1k
views
Tutorial:
Normality Test For JB (Jarque Bera) Test R Commander
Jarque-Bera-Test
R-Commander
updated 10 months ago by
Ram
43k • written 6.3 years ago by
helgasaraswati
▴ 10
5
votes
2
replies
3.1k
views
Tutorial:
Get GC Content from UCSC with perl script (mysql)
myql
ucsc
gc-content
perl
updated 10 months ago by
Ram
43k • written 6.9 years ago by
Shicheng Guo
★ 9.4k
7
votes
0
replies
3.0k
views
Tutorial:
On the concept of constant or intercept used in Differential Expression (DE) analysis
regression
limma
DESeq2
updated 11 months ago by
Ram
43k • written 7.9 years ago by
Antonio R. Franco
★ 5.1k
0
votes
0
replies
2.8k
views
Tutorial:
Autocorrelation With Breusch Godfrey Serial Correlation LM Test R Commander
LM-Test
R
Autocorrelation
Breusch-Godfrey
updated 10 months ago by
Ram
43k • written 6.3 years ago by
helgasaraswati
▴ 10
4
votes
2
replies
2.7k
views
Tutorial:
Building mosdepth on macOS
nim
mosdepth
updated 6 months ago by
GenoMax
140k • written 3.9 years ago by
ATpoint
81k
0
votes
1
reply
2.7k
views
Tutorial:
Clustering and results Display from PART II (PART III) - MeV software version
gene
R
updated 11 months ago by
Ram
43k • written 7.8 years ago by
majuang66
▴ 140
2
votes
3
replies
2.6k
views
Tutorial:
It's about the journey, and not the destination
R
network
updated 10 months ago by
Ram
43k • written 6.9 years ago by
theobroma22
★ 1.2k
3
votes
2
replies
2.6k
views
Tutorial:
Continuing Education (Pipelines): Best blogs, Online Lectures, Workshops, etc..
conferences
Workshops
updated 10 months ago by
Ram
43k • written 6.9 years ago by
jnowacki
▴ 100
1
vote
0
replies
2.5k
views
Tutorial:
GEO Data Mining (II) - Differential gene expression analysis and visualization with complete code sharing
geo
R
data-mining
differential-gene-expression
RNA-Seq
updated 9 months ago by
Ram
43k • written 14 months ago by
Novogene
▴ 410
0
votes
0
replies
2.4k
views
Tutorial:
Rembrandt Glioma Data Analysis (PART II) - Are Gender specific genes related to cancer ?
gene
R
Rembrandt
updated 11 months ago by
Ram
43k • written 7.7 years ago by
majuang66
▴ 140
14
votes
2
replies
2.4k
views
Tutorial:
Exploring OpenSNP - an RMarkdown report on crowdsourced genotypes and phenotypes
SNP
R
updated 11 months ago by
Ram
43k • written 8.0 years ago by
Jeremy Leipzig
22k
7
votes
3
replies
2.4k
views
Tutorial:
Automated dbSNP lookup by rsID position, plus genome build liftover
rsid
hg19
liftover
hg38
dbsnp
updated 11 months ago by
Randy H
▴ 110 • written 19 months ago by
Kevin Blighe
87k
0
votes
2
replies
2.4k
views
Tutorial:
COURSE: NGS variant analysis and interpretation for translational research
CNIO
course
translational
updated 11 months ago by
Ram
43k • written 7.5 years ago by
Folder40g
▴ 190
4
votes
2
replies
2.3k
views
Tutorial:
Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation
rRNA
RNAmmer
Genome
8 months ago by
Dr.Animo
▴ 80
3
votes
1
reply
2.3k
views
Tutorial:
Convert bam files to fastq in numbers as indicated in samtools flagstat stats.
samtools
bam
alignment
fastq
sequence
updated 10 months ago by
Ram
43k • written 6.8 years ago by
kirannbishwa01
★ 1.6k
4
votes
0
replies
2.3k
views
Tutorial:
Accurate prediction of active enhancers using PARE
ChIP-Seq
histone-modification
enhancer
updated 10 months ago by
Ram
43k • written 6.9 years ago by
Sachin Pundhir
▴ 100
2
votes
0
replies
2.3k
views
Tutorial:
How to do pathway analysis with transcriptomics data using ArrayAnalysis.org
transcriptomics
R
pathway-analysis
updated 11 months ago by
Ram
43k • written 7.7 years ago by
friederike.ehrhart
▴ 20
9
votes
5
replies
2.2k
views
Tutorial:
What is new in samtools release 1.5 [Solstice Release] (21st June 2017)
samtools
updated 10 months ago by
Ram
43k • written 6.7 years ago by
Istvan Albert
100k
7
votes
1
reply
2.2k
views
Tutorial:
A gentle introduction to biogo
sequence
golang
biogo
updated 10 months ago by
Ram
43k • written 6.4 years ago by
Botond Sipos
★ 1.7k
3
votes
0
replies
2.2k
views
Tutorial:
Deep Learning for Cancer Immunotherapy
keras
tensorflow
updated 10 months ago by
Ram
43k • written 6.1 years ago by
Jeremy Leipzig
22k
5
votes
0
replies
2.2k
views
Tutorial:
Installing multiprocessor-capable MEME to work with a Slurm job scheduler environment
slurm
meme
parallel
updated 10 months ago by
Ram
43k • written 6.5 years ago by
Alex Reynolds
35k
11
votes
7
replies
2.2k
views
Tutorial:
Sequence Alignment from Scratch with BWA
alignment
bwa
DNA
11 months ago by
barslmn
★ 2.1k
2
votes
5
replies
2.2k
views
Tutorial:
Building OMA database on SGE
oma
updated 11 months ago by
Ram
43k • written 7.7 years ago by
javier.herrero
▴ 10
0
votes
0
replies
2.2k
views
Tutorial:
Transforming (Transformation) Data LN, Log, SQRT In R Commander
R
updated 10 months ago by
Ram
43k • written 6.1 years ago by
helgasaraswati
▴ 10
191 results • Page
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Recent Votes
Comment: Average expression of a sample in single-cell data
A: Normalize FPKM values for cross-sample comparisons?
Answer: ColabFold
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Troubleshooting a REGENIE sex-stratified GWAS
ENVO Ontology to Annotate Plain Text
Answer: Seurat 5 integration
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Answer: Deeptools scale issue for plotHeatmap
by
Learner
• 0
Hi Devon, Thanks a lot for the reply. DNA methylation file has 19466838 lines while domains has 92409 lines.
Answer: why there is an asterisk symbol at the end of each proteins sequences offasta fi
by
Juke34
8.5k
It corresponds to stop codon but in theory GTF format does not have stop codon in CDS. Keep in mind that it exists stop codon reading th…
Comment: scRNAseq normalization
by
ATpoint
81k
That is an entirely different analysis and depends on the testing Framework. If you use the commonly-used Wilcox test or something like lim…
Answer: Haddock 2.4
by
Preeti
• 0
i have three different runs with haddock score of -75, -68, -61 . Which one is better among these( molecule 1 is same in all three ,only mo…
Comment: NGS/GATK pipeline returns too many variants
by
dhruti
• 0
@dodausp Did you ever find a reason for this? I am having the same problem
Comment: Troubleshooting a REGENIE sex-stratified GWAS
by
Corentin
▴ 600
Sex chromosomes are always a bit tricky to handle in associations studies. How many male cases and male controls you have for this phenoty…
Answer: Haddock 2.4
by
Preeti
• 0
I want to know that which results from haddock are good like I got highest haddock score of -75 .....is it a good haddock score or not
Comment: Beagle Phasing and Imputation
by
Duarte Molha
▴ 240
Hi @lchart Thank you for your answer. I coded my male sample as biallelelic homozygous as i was aware of limitations for allosomes.…
Comment: error in wigToBigWig while converting mappability to bedgraph
by
Dora
▴ 10
And I also change the chrom name in the .sizes file. That works perfect. Thank you very much!
Comment: scRNAseq normalization
by
sarahmanderni
▴ 100
Thanks for the response! I also was wondering to ask if you have found the log-norm also working fine in terms of downstream analysis like …
Answer: Subsetting Seurat object based on list of cell barcodes
by
fracarb8
★ 1.5k
`subset(seurat.obj_combined, cells = all_good_cells_rhemac10$V1)` You need to pass `cells` not `subset`. From the documentation: sub…
Answer: TCGA UUIDS to TCGA barcode (SampleID) in R
by
aUser
▴ 30
Great solutions on this page, the old web page has been replace with new one, so you need to use the new link, and it will work: old lin…
Comment: Issues With Cram -> Fastq from GTEx v8 WGS
by
Pierre Lindenbaum
160k
unless your cram in sorted on query rather than on coordinate, your cram must be first sort processed with collate: https://twitter.com/lh…
Answer: error in wigToBigWig while converting mappability to bedgraph
by
Pierre Lindenbaum
160k
remove the spaces from your "chrom" key variableStep chrom=NT_173277 span=5 or may be quote the chrom variableStep chrom="NT_173277.1 C…
Comment: DEG (Differential expression gene) analysis
by
dsull
★ 5.6k
Well, I guess expression could be measured from the DNA indirectly such as with RNA Pol II binding to DNA via ChIP-seq but then the OP shou…
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