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411 results • Page
5 of 9
Sort: Rank
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Votes
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61
votes
6
replies
9.5k
views
Tutorial:
Minimum Standards For Bioinformatics Command Line Tools
command-line
updated 14 months ago by
Ram
43k • written 10.7 years ago by
Medhat
9.7k
5
votes
0
replies
1.1k
views
Tutorial:
Finding individual motif occurrences with FIMO from the MEME suite
motif
meme
jaspar
fimo
updated 13 months ago by
Ram
43k • written 5.4 years ago by
ATpoint
82k
5
votes
2
replies
2.3k
views
Tutorial:
NCBI submissions: SRA and TSA
NCBI
TSA
SRA
RNA-Seq
updated 13 months ago by
Ram
43k • written 5.4 years ago by
saraoppenheim
▴ 50
6
votes
0
replies
1.6k
views
Tutorial:
NCBI dbVar releases updated human reference structural variation (SV) data files and tutorials
dbvar
structural-variation
updated 13 months ago by
Ram
43k • written 5.5 years ago by
lonphan
▴ 70
32
votes
4
replies
7.9k
views
Tutorial:
Fast LD computation from VCF files using tomahawk
ld
snp
vcf
vcftools
bcftools
updated 13 months ago by
Ram
43k • written 5.5 years ago by
firestar
★ 1.6k
58
votes
25
replies
40k
views
15 follow
Tutorial:
Protocol To Downlad TCGA Data From GDC
GDC
methylation
TCGA
updated 13 months ago by
Ram
43k • written 7.8 years ago by
Shicheng Guo
★ 9.4k
65
votes
15
replies
14k
views
Tutorial:
Which human reference genome should I use?
assembly
genome
alignment
updated 11 months ago by
Ram
43k • written 5.6 years ago by
finswimmer
16k
3
votes
4
replies
3.6k
views
Tutorial:
Gene Set Enrichment Analysis on T-BioInfo
gene
RNA-Seq
updated 11 months ago by
Ram
43k • written 5.5 years ago by
elia.brodsky
▴ 340
22
votes
2
replies
6.0k
views
Tutorial:
Use a workflow management tool to manage your computational pipelines
workflow-management
snakemake
pipeline
updated 12 months ago by
Ram
43k • written 7.5 years ago by
Eric Lim
★ 2.1k
1
vote
2
replies
3.3k
views
Tutorial:
Standalone BLAST error: UnexpectedTagClassByte
software-error
blast
updated 18 months ago by
Ram
43k • written 8.7 years ago by
Harry Detering
▴ 10
75
votes
13
replies
67k
views
10 follow
Tutorial:
Machine Learning For Prediction of Relapse in Cancer - Part 2 - Building A Random Forest Classifier
r
cancer
classification
updated 18 months ago by
Ram
43k • written 10.4 years ago by
Nicholas Spies
★ 1.2k
20
votes
4
replies
14k
views
Tutorial:
How To Install A Specific Cdf Package For Use In Bioconductor
bioconductor
affymetrix
updated 14 months ago by
Ram
43k • written 11.1 years ago by
Obi Griffith
20k
0
votes
0
replies
1.3k
views
Tutorial:
In the cloud - Guide to running VerifyBamID to estimate DNA sample contamination
sequence
cloud
dna
sequencing
updated 11 months ago by
Ram
43k • written 5.7 years ago by
corlinp
• 0
20
votes
2
replies
8.1k
views
Tutorial:
Creating a karyotype plot with genes using karyoploteR
karyoploteR
visualization
R
genome
updated 11 months ago by
Ram
43k • written 6.4 years ago by
bernatgel
★ 3.4k
2
votes
0
replies
1.4k
views
Tutorial:
Principal Component Analysis (PCA ON T-BIOINFO)
RNA-Seq
next-gen
updated 11 months ago by
Ram
43k • written 5.9 years ago by
elia.brodsky
▴ 340
1
vote
4
replies
3.4k
views
Tutorial:
Applying machine learning to NGS transcriptomic data
next-gen
RNA-Seq
updated 11 months ago by
Ram
43k • written 6.0 years ago by
elia.brodsky
▴ 340
3
votes
4
replies
4.5k
views
Tutorial:
gencore: a tool to reduce sequencing noises by generating consensus reads
consensus
OpenGene
sequencing-noise
updated 11 months ago by
Ram
43k • written 6.0 years ago by
chen
★ 2.5k
18
votes
2
replies
5.9k
views
Tutorial:
Update kraken databases
database
kraken
k-mer
python
updated 11 months ago by
Ram
43k • written 7.0 years ago by
Sej Modha
5.3k
2
votes
0
replies
1.5k
views
Tutorial:
Webinar: Extracting research evidence from publications
text-mining
ontology
pubmed
updated 11 months ago by
Ram
43k • written 6.2 years ago by
Maria_Levchenko
▴ 60
147
votes
34
replies
55k
views
17 follow
Tutorial:
Working with MAF files (Mutation Annotation Format) from the TCGA (The Cancer Genome Atlas)
music
cancer
tcga
mutation
maf
updated 14 months ago by
Ram
43k • written 11.0 years ago by
Cyriac Kandoth
6.0k
1
vote
0
replies
2.3k
views
Tutorial:
Tutorial DEAP 2.1 In DOS
deap2.1
R
updated 13 months ago by
Ram
43k • written 6.2 years ago by
helgasaraswati
▴ 10
0
votes
0
replies
3.6k
views
Tutorial:
SFA (Stochastic Frontier Analysis) STATA 14
R
updated 11 months ago by
Ram
43k • written 6.2 years ago by
helgasaraswati
▴ 10
0
votes
0
replies
1.6k
views
Tutorial:
PLS SEM (Partial Least Square Sructural Equation Modeling) Analysis WarpPLS 6
R
updated 11 months ago by
Ram
43k • written 6.2 years ago by
helgasaraswati
▴ 10
3
votes
0
replies
2.2k
views
Tutorial:
Deep Learning for Cancer Immunotherapy
keras
tensorflow
updated 11 months ago by
Ram
43k • written 6.2 years ago by
Jeremy Leipzig
22k
0
votes
0
replies
1.6k
views
Tutorial:
MWD (Mackinnon, White And Davidson) In R
R
updated 11 months ago by
Ram
43k • written 6.3 years ago by
helgasaraswati
▴ 10
0
votes
0
replies
2.2k
views
Tutorial:
Transforming (Transformation) Data LN, Log, SQRT In R Commander
R
updated 11 months ago by
Ram
43k • written 6.3 years ago by
helgasaraswati
▴ 10
14
votes
2
replies
2.4k
views
Tutorial:
Exploring OpenSNP - an RMarkdown report on crowdsourced genotypes and phenotypes
SNP
R
updated 12 months ago by
Ram
43k • written 8.1 years ago by
Jeremy Leipzig
22k
0
votes
0
replies
3.6k
views
Tutorial:
Park Test for Heteroskedasticity In R Commander
R
Park-Test
updated 11 months ago by
Ram
43k • written 6.3 years ago by
helgasaraswati
▴ 10
0
votes
0
replies
8.1k
views
Tutorial:
Multicollinearity VIF (Variance Inflation Factor) Analysis in Panel data EVIEWS 9
R
eviews
updated 11 months ago by
Ram
43k • written 6.3 years ago by
helgasaraswati
▴ 10
23
votes
19
replies
6.9k
views
10 follow
Tutorial:
MutScan: Detect important mutations by scanning FastQ files directly
fastq
mutation
cancer
target
updated 12 months ago by
Ram
43k • written 7.6 years ago by
chen
★ 2.5k
1
vote
0
replies
1.4k
views
Tutorial:
Fall 2017 Introduction to Human Genomics for Clinical Informaticists
genome
updated 11 months ago by
Ram
43k • written 6.3 years ago by
bdolin
▴ 90
0
votes
1
reply
1.8k
views
Tutorial:
Guide Tutorial DEAP 2.1 In Windows 7
DEAP2.1
R
stata
updated 13 months ago by
Ram
43k • written 6.3 years ago by
helgasaraswati
▴ 10
0
votes
1
reply
1.9k
views
Tutorial:
Nonparametric Regression STATA 15
STATA-15
Nonparametric-Regression
STATA
updated 11 months ago by
Ram
43k • written 6.3 years ago by
helgasaraswati
▴ 10
3
votes
3
replies
8.8k
views
Tutorial:
High Speed Downloading of SRA, SAM and Fastq Files
fastq
sam
Aspera-Connect
sra
updated 11 months ago by
Ram
43k • written 6.3 years ago by
Wenhu_Cao
▴ 100
2
votes
0
replies
6.9k
views
Tutorial:
How to - Install Python packages in a virtual environment (virtualenv)
ubuntu
cutadapt
virtualenv
python
windows
updated 11 months ago by
Ram
43k • written 6.4 years ago by
vimalkvn
▴ 320
0
votes
0
replies
2.9k
views
Tutorial:
Autocorrelation With Breusch Godfrey Serial Correlation LM Test R Commander
LM-Test
R
Autocorrelation
Breusch-Godfrey
updated 11 months ago by
Ram
43k • written 6.4 years ago by
helgasaraswati
▴ 10
0
votes
0
replies
3.1k
views
Tutorial:
Normality Test For JB (Jarque Bera) Test R Commander
Jarque-Bera-Test
R-Commander
updated 11 months ago by
Ram
43k • written 6.4 years ago by
helgasaraswati
▴ 10
0
votes
0
replies
1.4k
views
Tutorial:
Data Panel In R Commander
R
updated 11 months ago by
Ram
43k • written 6.4 years ago by
helgasaraswati
▴ 10
10
votes
1
reply
9.3k
views
Tutorial:
How to select reads with specific flag using samtools
next-gen-sequencing
updated 11 months ago by
Ram
43k • written 6.6 years ago by
imlituan
▴ 110
12
votes
1
reply
5.1k
views
Tutorial:
RepSeq data processing and analysis
immunology
tcr
repseq
sequencing
repertoire
updated 18 months ago by
Ram
43k • written 8.7 years ago by
mikhail.shugay
3.5k
2
votes
0
replies
2.1k
views
Tutorial:
How to display Agilent CGH array in IGV
IGV
CGH
updated 11 months ago by
Ram
43k • written 6.4 years ago by
sacha
★ 2.4k
3
votes
2
replies
8.8k
views
Tutorial:
Use fastp to preprocess FASTQ data with unique molecular identifer (UMI) integrated
FASTQ
UMI
fastp
updated 11 months ago by
Ram
43k • written 6.4 years ago by
chen
★ 2.5k
39
votes
6
replies
19k
views
Tutorial:
Creating chromosome karyotype plot with R and ggplot2
ggplot2
R
chromosome
karyotype
updated 11 months ago by
Ram
43k • written 6.7 years ago by
steve
★ 3.5k
15
votes
1
reply
7.1k
views
Tutorial:
A compilation of conversion tools for BED, SAM/BAM, psl, pslx, blast tabular and blast xml
psl
SAM
blast
BED
updated 11 months ago by
Ram
43k • written 6.5 years ago by
Joseph Hughes
★ 3.0k
5
votes
5
replies
7.0k
views
Tutorial:
use firehose_get to download TCGA data
tcga
RNA-Seq
updated 11 months ago by
Ram
43k • written 6.5 years ago by
jmzeng1314
▴ 130
7
votes
1
reply
2.2k
views
Tutorial:
A gentle introduction to biogo
sequence
golang
biogo
updated 11 months ago by
Ram
43k • written 6.5 years ago by
Botond Sipos
★ 1.7k
0
votes
1
reply
3.2k
views
Tutorial:
Accessing sequences using batch entrez
genome
updated 11 months ago by
Ram
43k • written 6.5 years ago by
mawia.martha
• 0
42
votes
16
replies
23k
views
15 follow
Tutorial:
Tutorial: Analyze exome Copy number variation (CNV) in single patient or in population.
GISTIC
varscan2
CNV
copy-number
updated 20 months ago by
Ram
43k • written 8.6 years ago by
Chirag Nepal
★ 2.4k
2
votes
0
replies
3.3k
views
Tutorial:
use the tool slicer to split big files (like FASTQ) to smaller files for parallel processing
opengene
slicer
fastq
splitter
updated 10 months ago by
Ram
43k • written 6.5 years ago by
chen
★ 2.5k
5
votes
2
replies
3.1k
views
Tutorial:
Get GC Content from UCSC with perl script (mysql)
myql
ucsc
gc-content
perl
updated 11 months ago by
Ram
43k • written 7.0 years ago by
Shicheng Guo
★ 9.4k
411 results • Page
5 of 9
Recent Votes
Comment: NGS forensics: how to know if data is fabricated
A: Hard time trying to calculate Allele Frequency and DP from Platypus
Answer: NGS forensics: how to know if data is fabricated
Answer: NGS forensics: how to know if data is fabricated
Comment: NGS forensics: how to know if data is fabricated
Answer: NGS forensics: how to know if data is fabricated
Comment: NGS forensics: how to know if data is fabricated
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Answer: Differential Expression using Isoseq-supplemented reference transcriptome
by
Gordon Smyth
★ 7.0k
> What is the best method to test for differential abundance at the isoform level? Salmon returns TPM values instead of the counts which Li…
Answer: Finding batch and outlayers
by
Tigran
• 0
![enter image description here][1] [1]: /media/images/aa60b9ef-b08c-4093-9f0d-fb656a5c
Comment: NGS forensics: how to know if data is fabricated
by
benformatics
3.9k
Can you post an IGV screenshot of what this looks like?
Comment: NGS forensics: how to know if data is fabricated
by
benformatics
3.9k
Yeah some of the Illumina machines pre-trim adapters (not sure if this is still the standard). I've also definitely also seen quality-trimm…
Comment: PDB related issue
by
noodle
▴ 530
You can typically find much more useful info in the cif file, for example what you've found is called '_atom_site.pdbx_PDB_ins_code ' and d…
Comment: PDB related issue
by
Mensur Dlakic
★ 27k
The best way to find out is to read the original paper. My guess is that the residue has been crystallized in alternative conformations, wh…
Answer: NGS forensics: how to know if data is fabricated
by
Mensur Dlakic
★ 27k
I share the opinion by @philippbayer I have seen enough questionable things in life and in science to keep me permanently jaded, but there…
Comment: How many reads for WGS Sequencing?
by
Mensur Dlakic
★ 27k
I downloaded the data in two files from the link you provided. With this command: megahit -1 ERR072246_1.fastq.gz -2 ERR072246_2.fastq…
Comment: How many reads for WGS Sequencing?
by
Mensur Dlakic
★ 27k
If you have Linux the assembly should work on your system, but 8 GB is generally not enough for assembling larger genomes.
Comment: How many reads for WGS Sequencing?
by
Mensur Dlakic
★ 27k
I think you might be getting stuck on less relevant parts of my exercise. The most important point was that nothing is wrong with the data.…
Comment: What does it mean single base resolution in sequencing?
by
dsull
★ 5.9k
Great comprehensive explanation and overview of the technologies -- with regards to sequencing assays, the one thing I'd add is SNV identif…
Answer: What does it mean single base resolution in sequencing?
by
dsull
★ 5.9k
I think that term means slightly different things in different contexts. For example, it's useful to profile mRNA modifications (e.g. m6a) …
Comment: Cannot process all the reads in a fast5 file?
by
chujie
• 0
Hi, I met the same problem, have you found the solution?
Answer: What does it mean single base resolution in sequencing?
by
LauferVA
4.2k
Hi @fe3e6f65 , In a single sentence, the answer to your question can be summarized as, "*the resolution of a genomic technology refers to …
Comment: PCA plot
by
LauferVA
4.2k
Without more context, we cannot interpret this PCA plot. There are many possibilities. In addition, this question is basic enough that it w…
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