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232 results • Page
3 of 5
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Votes
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4
votes
0
replies
1.4k
views
Tutorial:
NIH CDE browser for TCGA clinical data CDE codes
nih
tcga
metadata
cde
updated 12 days ago by
Ram
38k • written 3.0 years ago by
Kevin Blighe
84k
12
votes
1
reply
4.8k
views
Tutorial:
scRNA-seq CITE-seq-count bioinformatics
CITE-seq-count
scRNA-seq
RNA-Seq
updated 12 days ago by
Ram
38k • written 3.0 years ago by
colindaven
4.6k
9
votes
4
replies
9.0k
views
Tutorial:
Using the MinION MinKNOW software on Ubuntu 1604
long-reads
oxford-nanopore
minion
updated 12 days ago by
Ram
38k • written 3.7 years ago by
colindaven
4.6k
0
votes
0
replies
987
views
Tutorial:
Training GeneMark-EP+ ab-initio tool
abinitio
training
genemark
annotation
updated 12 days ago by
Ram
38k • written 3.1 years ago by
Juke34
7.7k
2
votes
1
reply
2.4k
views
Tutorial:
How to extract and filter SNP data from the genotyping-by-sequencing (GBS) data in vcf format using bcftools
bcftools
SNP-Filtering
VCF
updated 12 days ago by
Ram
38k • written 3.1 years ago by
Asad Prodhan
▴ 10
5
votes
0
replies
2.6k
views
Tutorial:
How to run CWL with Nextflow
cwl
nextflow
updated 12 days ago by
Ram
38k • written 3.1 years ago by
steve
★ 3.3k
5
votes
2
replies
2.0k
views
Tutorial:
Using Bedtools Closest (closestBed) to make distance histograms of protein binding frequency near all types of pre-RNA junctions (e.g. exon-intron an…
preRNA
closestBed
bedtools-closest
bedtools
updated 12 days ago by
Ram
38k • written 4.2 years ago by
linuxborg2
▴ 10
50
votes
3
replies
4.0k
views
Tutorial:
[[ Please read before posting a question ::: How To Ask A Good Question ]]
how-to
updated 12 days ago by
Ram
38k • written 4.2 years ago by
ATpoint
70k
19
votes
9
replies
6.0k
views
8 follow
Tutorial:
Interactive Perl Learning
perl
updated 27 days ago by
Ram
38k • written 9.8 years ago by
Medhat
9.5k
276
votes
39
replies
164k
views
29 follow
Tutorial:
How to download raw sequence data from GEO/SRA
fastq
SRA
bam
GEO
updated 2 days ago by
Ram
38k • written 8.6 years ago by
Obi Griffith
20k
64
votes
26
replies
11k
views
7 follow
Tutorial:
Parallel processing in R
biocparallel
mclapply
foreach
R
updated 12 days ago by
Ram
38k • written 5.5 years ago by
Kevin Blighe
84k
34
votes
15
replies
5.0k
views
6 follow
Tutorial:
How to do data cleaning for VCF genetic file
vcf
updated 12 days ago by
Ram
38k • written 3.8 years ago by
Shicheng Guo
★ 9.3k
20
votes
4
replies
2.2k
views
Tutorial:
Bash One-liners collection on Github
bash
linux
shell
updated 12 days ago by
Ram
38k • written 3.9 years ago by
nim.1111.ou
▴ 180
14
votes
7
replies
5.4k
views
Tutorial:
Visualization of ChIP-Seq peak overlaps using HOMER mergePeaks and UpSetR
ChIP-Seq
peaks
R
HOMER
updated 12 days ago by
Ram
38k • written 6.9 years ago by
steve
★ 3.3k
2
votes
0
replies
3.8k
views
Tutorial:
Calculation of TSS Scores for ATAC-seq Data
next-gen-sequencing
updated 12 days ago by
Ram
38k • written 3.7 years ago by
Sael
▴ 20
0
votes
0
replies
896
views
Tutorial:
Apply ALoFT to identify loss-of-function somatic or germline variants
ALoFT
updated 12 days ago by
Ram
38k • written 3.8 years ago by
Shicheng Guo
★ 9.3k
16
votes
11
replies
13k
views
7 follow
Tutorial:
retrieve full TCGA datasets from cBioportal with R
TCGA
RNA-seq
data-retrieval
cBioportal
R
updated 12 days ago by
Ram
38k • written 6.4 years ago by
TriS
★ 4.6k
10
votes
5
replies
18k
views
Tutorial:
Y-DNA and mtDNA Haplogroup Predictor
haplogroup
updated 12 days ago by
Ram
38k • written 4.7 years ago by
Shicheng Guo
★ 9.3k
34
votes
15
replies
18k
views
12 follow
Tutorial:
TCGA UUIDS to TCGA barcode (SampleID) in R
next-gen
GDC
R
TCGA
updated 11 days ago by
Ram
38k • written 6.5 years ago by
martinguerrerog89
▴ 310
6
votes
3
replies
4.1k
views
Tutorial:
Principles and Workflow of 16S/18S/ITS Amplicon Sequencing
alignment
sequencing
RNA-seq
gene
updated 11 days ago by
Ram
38k • written 4.4 years ago by
contact
▴ 40
0
votes
0
replies
924
views
Tutorial:
Introduction to Gen3 Webinar
gen3
open-source
data-commons
big-data
updated 11 days ago by
Ram
38k • written 4.1 years ago by
Danielle
▴ 310
4
votes
2
replies
3.3k
views
Tutorial:
Introduce OpenGene: an open source library for processing NGS data
NGS
sequencing
Julia
OpenGene
updated 11 days ago by
Ram
38k • written 7.1 years ago by
chen
★ 2.4k
28
votes
4
replies
3.7k
views
Tutorial:
Modern Statistics for Modern Biology
statistics
updated 11 days ago by
Ram
38k • written 4.2 years ago by
Jean-Karim Heriche
26k
60
votes
6
replies
8.9k
views
Tutorial:
Minimum Standards For Bioinformatics Command Line Tools
command-line
updated 27 days ago by
Ram
38k • written 9.6 years ago by
Medhat
9.5k
4
votes
0
replies
589
views
Tutorial:
Finding individual motif occurrences with FIMO from the MEME suite
motif
meme
jaspar
fimo
updated 9 days ago by
Ram
38k • written 4.3 years ago by
ATpoint
70k
5
votes
2
replies
2.0k
views
Tutorial:
NCBI submissions: SRA and TSA
NCBI
TSA
SRA
RNA-Seq
updated 9 days ago by
Ram
38k • written 4.3 years ago by
saraoppenheim
▴ 50
6
votes
0
replies
1.3k
views
Tutorial:
NCBI dbVar releases updated human reference structural variation (SV) data files and tutorials
dbvar
structural-variation
updated 9 days ago by
Ram
38k • written 4.4 years ago by
lonphan
▴ 70
32
votes
4
replies
6.4k
views
Tutorial:
Fast LD computation from VCF files using tomahawk
ld
snp
vcf
vcftools
bcftools
updated 9 days ago by
Ram
38k • written 4.4 years ago by
firestar
★ 1.5k
58
votes
25
replies
36k
views
15 follow
Tutorial:
Protocol To Downlad TCGA Data From GDC
GDC
methylation
TCGA
updated 9 days ago by
Ram
38k • written 6.7 years ago by
Shicheng Guo
★ 9.3k
1
vote
2
replies
2.9k
views
Tutorial:
Standalone BLAST error: UnexpectedTagClassByte
software-error
blast
updated 5 months ago by
Ram
38k • written 7.6 years ago by
Harry Detering
▴ 10
74
votes
13
replies
65k
views
10 follow
Tutorial:
Machine Learning For Prediction of Relapse in Cancer - Part 2 - Building A Random Forest Classifier
r
cancer
classification
updated 4 months ago by
Ram
38k • written 9.4 years ago by
Nicholas Spies
★ 1.2k
20
votes
4
replies
13k
views
Tutorial:
How To Install A Specific Cdf Package For Use In Bioconductor
bioconductor
affymetrix
updated 4 weeks ago by
Ram
38k • written 10.0 years ago by
Obi Griffith
20k
145
votes
34
replies
51k
views
17 follow
Tutorial:
Working with MAF files (Mutation Annotation Format) from the TCGA (The Cancer Genome Atlas)
music
cancer
tcga
mutation
maf
updated 4 weeks ago by
Ram
38k • written 9.9 years ago by
Cyriac Kandoth
5.9k
0
votes
1
reply
1.6k
views
Tutorial:
Guide Tutorial DEAP 2.1 In Windows 7
DEAP2.1
R
stata
updated 9 days ago by
Ram
38k • written 5.2 years ago by
helgasaraswati
▴ 10
12
votes
1
reply
4.7k
views
Tutorial:
RepSeq data processing and analysis
immunology
tcr
repseq
sequencing
repertoire
updated 5 months ago by
Ram
38k • written 7.6 years ago by
mikhail.shugay
3.5k
42
votes
16
replies
21k
views
15 follow
Tutorial:
Tutorial: Analyze exome Copy number variation (CNV) in single patient or in population.
GISTIC
varscan2
CNV
copy-number
updated 7 months ago by
Ram
38k • written 7.5 years ago by
Chirag Nepal
★ 2.3k
12
votes
4
replies
1.8k
views
Tutorial:
Tutorials for Library Normalization in DESeq2 and EdgeR
EdgeR
DESeq2
updated 3 days ago by
Ram
38k • written 5.5 years ago by
KVC_bioinfo
▴ 570
24
votes
15
replies
7.9k
views
8 follow
Tutorial:
Syllabus To Learn Bioinformatics From Online Video Resources
course
training
mooc
updated 4 weeks ago by
Ram
38k • written 10.2 years ago by
Medhat
9.5k
53
votes
5
replies
14k
views
6 follow
Tutorial:
Machine Learning For Cancer Classification - Part 4 - Plotting A Kaplan-Meier Curve For Survival Analysis
r
updated 5 months ago by
Ram
38k • written 9.3 years ago by
Nicholas Spies
★ 1.2k
7
votes
2
replies
11k
views
Tutorial:
Howto use NCBI programs behind a HTTP proxy
blast-plus
HTTP-proxy
SRA-toolkit
updated 8 months ago by
Ram
38k • written 7.1 years ago by
piet
★ 1.8k
11
votes
6
replies
4.5k
views
Tutorial:
sharing some naive codes for microarray normalization in R with whom are too new in R alike me
R
updated 8 months ago by
Ram
38k • written 7.1 years ago by
fi1d18
★ 4.1k
33
votes
16
replies
15k
views
10 follow
Tutorial:
Machine Learning For Cancer Classification - Part 3 - Predicting With A Random Forest Classifier
machine-learning
classification
updated 25 days ago by
Ram
38k • written 9.3 years ago by
Obi Griffith
20k
15
votes
2
replies
6.5k
views
Tutorial:
Genotype And Snp Calling Review Papers
snp
updated 4 weeks ago by
Ram
38k • written 10.6 years ago by
Istvan Albert
97k
89
votes
19
replies
30k
views
12 follow
Tutorial:
Machine Learning For Cancer Classification - Part 1 - Preparing The Data Sets
microarray
bioconductor
expression
classification
updated 25 days ago by
Ram
38k • written 9.4 years ago by
Obi Griffith
20k
19
votes
4
replies
8.4k
views
Tutorial:
Rna Seq Experimental Design For Measuring Differential Gene Expression
RNA-seq
updated 4 weeks ago by
Ram
38k • written 10.1 years ago by
Istvan Albert
97k
6
votes
11
replies
4.5k
views
6 follow
Tutorial:
Add count numbers to headers in a fasta file
genome
updated 6 weeks ago by
Ram
38k • written 6.3 years ago by
wu.zhiqiang.1020
▴ 50
15
votes
2
replies
2.7k
views
Tutorial:
Introduction to bedtools.
bedtools
updated 17 days ago by
Ram
38k • written 8.4 years ago by
Aaronquinlan
11k
30
votes
14
replies
15k
views
8 follow
Tutorial:
Installation of the MuSiC suite on unsupported Linux distributions
genome-music
linux
smg
updated 4 weeks ago by
Ram
38k • written 10.1 years ago by
Cyriac Kandoth
5.9k
142
votes
21
replies
29k
views
12 follow
Tutorial:
A few words for R beginners
Swirl
R
updated 10 months ago by
Ram
38k • written 8.3 years ago by
Parham
★ 1.6k
17
votes
3
replies
11k
views
Tutorial:
bedGraphToBigWig Tutorial and Report
bedGraphToBigWig
updated 8 months ago by
Ram
38k • written 7.1 years ago by
Shicheng Guo
★ 9.3k
232 results • Page
3 of 5
Recent Votes
Create Interval List for Picard CollectRNASeqmetrics
Answer: multiallelic variants
Answer: LIMMA calculates identical adj.P.Val for different proteins from proteomics
Comment: Hard clip fastq
Answer: Hard clip fastq
Answer: Hard clip fastq
Answer: Hard clip fastq
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Answer: Somatic truth set
by
samuel
▴ 180
I think I have found an naswer to my own question. Should anyone have the same question as of March 2023 the relevant data and information…
Answer: GetBM - GERP conservation score for GRCm39
by
Kyle
• 0
Final solution thanks to Ben's help:: # convert df to Grange. snp_gr <-makeGRangesFromDataFrame(BM_SNPs, seqnames.field = "seqnam…
Comment: GetBM - GERP conservation score for GRCm39
by
Kyle
• 0
Perfect answer, thanks Ben!
Answer: MapSplice2 gives error if the thread count (-p value) is greater than 2
by
vishal.koparde
▴ 10
Any updates??
Comment: how to know what adapter sequences to trim for RNA-seq?
by
lunarskye222
• 0
Do you happen to know if the middle part of this udi barcode (GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTCTACATATCTCG) is also part of the TruSeq a…
Comment: Hard clip fastq
by
GenoMax
127k
If you simply want the reads to be compatible in length then do not adapter trim.
Comment: Hard clip fastq
by
samuel
▴ 180
@ATpoint, so no adapter trimming first? Just trim the raw fastq?
Answer: Confused on strandedness, what are antisense transcripts?
by
dsull
★ 4.0k
Think of it on the DNA level: If the mRNA made is the same sequence as the "sense" DNA strand (except U's instead of T's), it is a "sense" …
Comment: Protein name in GenBank
by
GenoMax
127k
If you must do this programmatically then collect all cases where things differ in order of words (or number of words) like the example abo…
Answer: Hard clip fastq
by
GenoMax
127k
You can also use `reformat.sh` from [**BBMap suite**][1] as follows reformat.sh -Xmx2g in1=R1.fq.gz in2=R2.fq.gz out1=R1_trim.fq.gz …
Answer: Hard clip fastq
by
ATpoint
70k
Use `seqtk trimfq`. It makes sense to trim first to your desired length and then run identical downstream processing for a fair comparison.…
Comment: Protein name in GenBank
by
Mensur Dlakic
★ 23k
I think you either take time to do it properly, or you will end up missing some proteins. BLAST sequence search, even on 1500 genomes, can …
Comment: Log2 FC Threshold
by
ATpoint
70k
Since OP is using GEO2R which uses limma the appropriate function (need to run manually, GEO2R does not support) is `limma::treat()` rather…
Answer: Adding median value to VlnPlot in Seurat
by
Ming Tommy Tang
★ 2.9k
If you know ggplot2, you can `get_expression_data` function in here https://divingintogeneticsandgenomics.rbind.io/post/how-to-do-gene-corr…
Answer: how to know what adapter sequences to trim for RNA-seq?
by
Ming Tommy Tang
★ 2.9k
You may use fastp which detect adaptors by itself https://github.com/OpenGene/fastp#adapters
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