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358 results • Page
3 of 8
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Votes
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19
votes
2
replies
3.1k
views
Tutorial:
Beginner's Handbook to Next Generation Sequencing
NGS
updated 27 days ago by
Ram
39k • written 6.2 years ago by
support
▴ 640
19
votes
9
replies
6.1k
views
8 follow
Tutorial:
Interactive Perl Learning
perl
updated 3 months ago by
Ram
39k • written 10.0 years ago by
Medhat
9.6k
18
votes
2
replies
5.5k
views
Tutorial:
Update kraken databases
database
kraken
k-mer
python
updated 26 days ago by
Ram
39k • written 6.1 years ago by
Sej Modha
5.2k
18
votes
40
replies
16k
views
16 follow
Tutorial:
Easy way to run easily orthoMCL (Copy & paste)
all-v-all
orthomcl
updated 12 weeks ago by
Ram
39k • written 6.9 years ago by
Esaie
▴ 170
18
votes
3
replies
12k
views
Tutorial:
bedGraphToBigWig Tutorial and Report
bedGraphToBigWig
updated 10 months ago by
Ram
39k • written 7.3 years ago by
Shicheng Guo
★ 9.3k
18
votes
2
replies
9.6k
views
Tutorial:
Video: RNA-Seq Alignment and Visualization using Galaxy and IGB
RNA-Seq
Galaxy
IGB
updated 14 months ago by
Ram
39k • written 8.6 years ago by
Nowlan Freese
▴ 860
18
votes
22
replies
7.5k
views
10 follow
Tutorial:
Create de novo repeat library
de-novo
repeat
annotation
updated 12 weeks ago by
Ram
39k • written 3.5 years ago by
Juke34
7.9k
17
votes
13
replies
1.7k
views
Tutorial:
Screen shots of text (please don't)!
meta
updated 27 days ago by
Ram
39k • written 6.2 years ago by
Michael
52k
16
votes
7
replies
13k
views
Tutorial:
Integrating VDJ sequencing data with Seurat
VDJ
Seurat
sc-RNAseq
clonotyping
updated 12 weeks ago by
Ram
39k • written 4.0 years ago by
atakanekiz
▴ 310
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 weeks ago by
Ram
39k • written 6.6 years ago by
TriS
★ 4.6k
16
votes
9
replies
4.7k
views
Tutorial:
TCGA transcriptome data to R (DESeq2)
TCGA
GDC
DESeq2
updated 12 months ago by
dk0319
▴ 70 • written 18 months ago by
Barry Digby
★ 1.1k
16
votes
0
replies
12k
views
Tutorial:
Workshop - Analysis Of Next Generation Sequencing Data
RNA-seq
updated 3 months ago by
Ram
39k • written 11.2 years ago by
David Langenberger
9.9k
16
votes
6
replies
5.8k
views
Tutorial:
How to make your snakefiles self-documenting
snakemake
updated 8 weeks ago by
Ram
39k • written 6.6 years ago by
Botond Sipos
★ 1.7k
16
votes
5
replies
8.5k
views
Tutorial:
Using The Biomart Perl Api For Simple Queries
api
perl
biomart
updated 3 months ago by
Ram
39k • written 10.7 years ago by
Obi Griffith
20k
16
votes
11
replies
7.5k
views
Tutorial:
How to Use Biostars, Part II: Post types, Deleting, (Un)Subscribing, Linking and Bookmarking
meta
how-to
documentation
12 weeks ago by
Ram
39k
15
votes
4
replies
4.2k
views
Tutorial:
RNASeq tutorial for gene differential expression analysis
Transcriptomics
bioconductor
RNA-Seq
R
updated 12 weeks ago by
Ram
39k • written 2.9 years ago by
Thind amarinder
▴ 310
15
votes
5
replies
14k
views
Tutorial:
How to create a mutation lolliplot with GenVisR
bioconductor
graphics
R
genvisr
updated 8 weeks ago by
Ram
39k • written 7.0 years ago by
Obi Griffith
20k
15
votes
2
replies
2.7k
views
Tutorial:
Introduction to bedtools.
bedtools
updated 3 months ago by
Ram
39k • written 8.6 years ago by
Aaronquinlan
12k
15
votes
3
replies
4.3k
views
Tutorial:
NCBI blast tutorial
ncbi
blast
updated 8 weeks ago by
Ram
39k • written 7.1 years ago by
Eric Normandeau
11k
15
votes
1
reply
2.9k
views
Tutorial:
Current Topics in Genome Analysis 2016 (collection of educational lectures)
genomics
training
lectures
workshop
updated 8 weeks ago by
Ram
39k • written 7.1 years ago by
Malachi Griffith
19k
15
votes
1
reply
6.4k
views
Tutorial:
A compilation of conversion tools for BED, SAM/BAM, psl, pslx, blast tabular and blast xml
psl
SAM
blast
BED
updated 21 days ago by
Ram
39k • written 5.6 years ago by
Joseph Hughes
★ 3.0k
15
votes
0
replies
6.4k
views
Tutorial:
Introduction To Ngs Bioinformatics By The Bioinformatics Team At The University Of Texas
course
training
updated 3 months ago by
Ram
39k • written 11.0 years ago by
Istvan Albert
98k
15
votes
2
replies
1.6k
views
Tutorial:
Germline variant calling pipeline using Snakemake
snakemake
GATK
germline_variant_calling
updated 7 months ago by
brunobsouzaa
▴ 810 • written 20 months ago by
nhaus
▴ 280
15
votes
5
replies
11k
views
6 follow
Tutorial:
Easy way to do GO enrichment in R
enrichr
RNA-Seq
gene
R
updated 3 months ago by
Ram
39k • written 5.5 years ago by
ahmad mousavi
▴ 750
15
votes
2
replies
6.5k
views
Tutorial:
Genotype And Snp Calling Review Papers
snp
updated 3 months ago by
Ram
39k • written 10.8 years ago by
Istvan Albert
98k
14
votes
2
replies
2.2k
views
Tutorial:
Exploring OpenSNP - an RMarkdown report on crowdsourced genotypes and phenotypes
SNP
R
updated 9 weeks ago by
Ram
39k • written 7.2 years ago by
Jeremy Leipzig
21k
14
votes
2
replies
3.0k
views
Tutorial:
Methylation Analysis Tutorial in R_part2
cancer
methylation
RNA-Seq
R
updated 12 weeks ago by
Ram
39k • written 2.7 years ago by
Hamid Ghaedi
2.9k
14
votes
9
replies
4.3k
views
6 follow
Tutorial:
Setting up Aspera Connect (ascp) on Linux and macOS
aspera
ascp
updated 4 weeks ago by
sjlee4019
• 0 • written 11 months ago by
ATpoint
72k
14
votes
0
replies
9.0k
views
Tutorial:
How to generate PCA plot and heatmaps in R
heatmap
PCA
RNA-Seq
R
updated 8 weeks ago by
Ram
39k • written 6.7 years ago by
Ming Tommy Tang
★ 2.9k
14
votes
7
replies
5.6k
views
Tutorial:
Visualization of ChIP-Seq peak overlaps using HOMER mergePeaks and UpSetR
ChIP-Seq
peaks
R
HOMER
updated 12 weeks ago by
Ram
39k • written 7.1 years ago by
steve
★ 3.3k
14
votes
2
replies
6.2k
views
Tutorial:
ChIP-seq analysis tutorial
ChIP-Seq
updated 9 weeks ago by
Ram
39k • written 7.8 years ago by
Ming Tommy Tang
★ 2.9k
14
votes
0
replies
8.0k
views
Tutorial:
Video: ChIP-Seq Analysis and Visualization using Galaxy and IGB.
IGB
ChIP-Seq
Galaxy
MACS
RNA-Seq
updated 14 months ago by
Ram
39k • written 8.4 years ago by
Nowlan Freese
▴ 860
13
votes
3
replies
4.7k
views
Tutorial:
Video: Visualization of whole genome DNA methylation data in IGB
Bismark
BS-Seq
RNA-Seq
IGB
updated 12 months ago by
Ram
39k • written 8.2 years ago by
Nowlan Freese
▴ 860
13
votes
6
replies
5.3k
views
Tutorial:
Trim & align paired-end reads in a single pass
align
trim
fastq
pipe
paired-end
updated 8 weeks ago by
Ram
39k • written 7.0 years ago by
dariober
14k
12
votes
0
replies
7.4k
views
Tutorial:
Plot average methylation levels across TSS region
bedtools
RRBS
R
methylation
updated 14 months ago by
Ram
39k • written 8.4 years ago by
TriS
★ 4.6k
12
votes
1
reply
2.2k
views
Tutorial:
PCR Primer or Primer+Probe design
pcr
probe
rt-pcr
qpcr
primer
updated 2.0 years ago by
jared.andrews07
★ 14k • written 2.0 years ago by
Kevin Blighe
85k
12
votes
11
replies
6.7k
views
Tutorial:
How to upload your RNA-Seq data to NCBI Sequence Read Archive (SRA)
NCBI
Bioproject
SRA
BioSample
updated 28 days ago by
Ram
39k • written 6.2 years ago by
CandiceChuDVM
★ 2.4k
12
votes
1
reply
4.7k
views
Tutorial:
RepSeq data processing and analysis
immunology
tcr
repseq
sequencing
repertoire
updated 7 months ago by
Ram
39k • written 7.8 years ago by
mikhail.shugay
3.5k
12
votes
4
replies
4.7k
views
Tutorial:
*FREE course* Bioinformatics for Biologists: An Introduction to Linux, Bash Scripting, and R
linux
R
updated 3 months ago by
Ram
39k • written 2.3 years ago by
garden_giessen
▴ 120
12
votes
1
reply
5.0k
views
Tutorial:
scRNA-seq CITE-seq-count bioinformatics
CITE-seq-count
scRNA-seq
RNA-Seq
updated 12 weeks ago by
Ram
39k • written 3.2 years ago by
colindaven
4.9k
12
votes
5
replies
7.7k
views
Tutorial:
How To Install BioPerl Without Root Privileges in Ubuntu/Linxu
bioperl
updated 8 weeks ago by
Ram
39k • written 7.0 years ago by
Shicheng Guo
★ 9.3k
12
votes
0
replies
2.2k
views
Tutorial:
Long versus wide data for plotting genomics data in R.
ggplot2
tidyverse
data.table
R
updated 12 weeks ago by
Ram
39k • written 2.8 years ago by
rpolicastro
12k
12
votes
5
replies
1.9k
views
Tutorial:
FASTA file split
fasta
updated 12 weeks ago by
Ram
39k • written 3.0 years ago by
Juke34
7.9k
12
votes
4
replies
1.9k
views
Tutorial:
Tutorials for Library Normalization in DESeq2 and EdgeR
EdgeR
DESeq2
updated 10 weeks ago by
Ram
39k • written 5.7 years ago by
KVC_bioinfo
▴ 590
12
votes
7
replies
4.8k
views
Tutorial:
STARsolo config for 10x Chromium v1, v2, v3
Chromium
10x
STARsolo
STAR
updated 12 weeks ago by
Ram
39k • written 2.7 years ago by
Kevin Blighe
85k
12
votes
1
reply
2.7k
views
Tutorial:
Dealing with nanopore fast5 files compressed with vbz
hdf5
nanopore
fast5
vbz
MinKNOW
updated 9 months ago by
Assa Yeroslaviz
★ 1.8k • written 17 months ago by
dariober
14k
12
votes
20
replies
12k
views
10 follow
Tutorial:
Associating VDJ clonotyping data with scRNA-seq in Seurat
single-cell
RNA-Seq
seurat
TCR
updated 12 weeks ago by
Ram
39k • written 4.0 years ago by
jared.andrews07
★ 14k
12
votes
17
replies
2.3k
views
Tutorial:
How to find the mapping percentages for data deposited in the Zaire ebolavirus bioproject from the 2014 outbreak
ebola
bwa
updated 5 months ago by
Ram
39k • written 8.0 years ago by
Istvan Albert
98k
12
votes
31
replies
5.1k
views
6 follow
Tutorial:
gene set filter/selection for training ab initio annotation tools
geneset
genome
gene
abinitio
updated 3 months ago by
Ram
39k • written 3.8 years ago by
Juke34
7.9k
12
votes
2
replies
1.1k
views
Tutorial:
Factors in R - How do they work, and how did I break my data?
R
updated 12 weeks ago by
Ram
39k • written 2.2 years ago by
rpolicastro
12k
358 results • Page
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Recent Votes
Comment: Convert SAM to BAM
A: How Can I Get The Human Chromosome Centromere Position And Chromosome Length In
Comment: Differences in GTF files hg19 and hg38
Answer: plyranges:: summarise() not recognizing previous summarized column (counts)
NM_transcript ID gene identification
Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
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Comment: Limma returned only positive logFC values
by
Gordon Smyth
★ 6.1k
No, the updated code is no more correct than your original code. Before you undertake any differential expression analysis, you need to ha…
Comment: Differences in GTF files hg19 and hg38
by
heureuse
• 0
Thank you. Noted
Answer: Adjusting for batch effect and covariates with ComBat
by
zahra.elahi
• 0
For your first question that is "Shouldn't PCA analysis of combat_tpm look more homogenous than the original dataset?", NO, because you inc…
Answer: plyranges:: summarise() not recognizing previous summarized column (counts)
by
Alewa
▴ 120
solved, thanks! ``` #calculate the proportions of cpgs per chrom counts_cpgr <- cpgr %>% group_by(seqnames) %>% summarise(cnts = n()) count…
Comment: Limma returned only positive logFC values
by
melissachua90
▴ 40
Thank you for your comments. I've updated my code: group <- factor(type, levels=c("1a", "1b", "1c", "2a", "2b", "2c")) design <- m…
Comment: Creating a local version of Clustered NR database
by
GenoMax
130k
> One idea is to provide just the representative sequences as a first > pass. This seems reasonable since it should capture significant pa…
Comment: pal2nal -nogap -nomismatch options not working
by
Marie
• 0
Hi, did you end up solving this? I am running into the same issue. Marie
Comment: How to get information about promoter from bulk-RNAseq?
by
camillab.
▴ 130
and what about enhancer? is it possible to do it from a bulk-RNAseq?
Comment: How to get information about promoter from bulk-RNAseq?
by
camillab.
▴ 130
yes! clearly the terminology on my side needs to improved!
Comment: How to get information about promoter from bulk-RNAseq?
by
rpolicastro
12k
Generally speaking, most promoters only initiate transcription for a single gene, with a single gene potentially having multiple promoters …
Answer: How to get information about promoter from bulk-RNAseq?
by
Trivas
★ 1.2k
I'd probably select the genes of interest from your bulk RNA-seq results then use the UCSC table browser to get the sequence upstream of th…
Comment: How to add annotation columns with specific colors to the heatmap?
by
Ram
39k
Show us your exact code - it is quite easy to tweak colors in ComplexHeatmap with the `col=` argument.
Comment: VCF file CSQ flag
by
Ram
39k
True, but it's not technically impossible to annotate GVCFs, which is why I did not address that point.
Comment: Creating a local version of Clustered NR database
by
PeterC_NCBI
▴ 260
@genomax Sorry for the delay in reply. We're still working out the details of what exactly to provide. One idea is to provide just the rep…
Comment: Shannon's Entropy by Sliding Window in R
by
rohitsatyam102
▴ 690
Hi Were u able to achieve this?
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