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183 results • Page
3 of 4
Sort: Views
Rank
Views
Votes
Replies
0
votes
2
replies
194
views
BLAST using both nucleotides and taxonomic local databases
blast
ncbi
taxid
taxonomy
updated 1 day ago by
GenoMax
141k • written 1 day ago by
Begonia_pavonina
▴ 150
0
votes
2
replies
193
views
Result of running of p3_in.pl
primer3
updated 4 days ago by
GenoMax
141k • written 5 days ago by
nasri
• 0
0
votes
0
replies
193
views
Job:
Ensembl Outreach Project Leader
ebi
embl
genomics
ensembl
4 days ago by
Ben_Ensembl
★ 2.4k
0
votes
1
reply
191
views
Network Alignment
plugin
Cytoscape
CytoMCS
updated 2 days ago by
Scooter
▴ 280 • written 3 days ago by
Akash D
▴ 40
1
vote
1
reply
187
views
Herald:
The Biostar Herald for Tuesday, April 23, 2024
herald
updated 3 days ago by
Pierre Lindenbaum
161k • written 3 days ago by
Biostar
2.7k
3
votes
3
replies
183
views
genome assembly records not present in assembly_summary.txt
ncbi
bacteria
assembly
updated 22 hours ago by
GenoMax
141k • written 1 day ago by
sapuizait
▴ 10
6
votes
3
replies
183
views
Interpretting IGV output
IGV
updated 5 days ago by
Carlo Yague
8.7k • written 5 days ago by
analyst
▴ 30
2
votes
1
reply
180
views
Finding orthologs between genome error
OMA
OMAbrowser
updated 2 days ago by
Adrian Altenhoff
★ 1.1k • written 2 days ago by
hemantcnaik
• 0
0
votes
2
replies
180
views
Help with Base quality Score Recalibration (BQSR) using GATK
GATK
BQSR
4 days ago by
sainavyav22
• 0
0
votes
2
replies
179
views
Rare Disease Variant Pathway Analysis
Pathway-analysis
updated 13 hours ago by
Ram
43k • written 1 day ago by
The_PyPanda
▴ 10
0
votes
1
reply
175
views
homology modelling using swiss model
homology-modeling
swiss-model
updated 5 days ago by
colindaven
6.4k • written 5 days ago by
Ayush
• 0
1
vote
1
reply
169
views
Failed kmer content
kmer
illumina
ngs
updated 3 days ago by
Ram
43k • written 4 days ago by
Kasturi
• 0
1
vote
1
reply
163
views
ScRNAseq-How to correctly choose cell type marker genes
cellAssign
cell-markers
updated 1 day ago by
Ram
43k • written 1 day ago by
Francesco
▴ 10
0
votes
0
replies
162
views
Forum:
Improvement on automatic annotation of single-cell RNA-seq data from the literature using LLM
annotation
scRNA
llm
4 days ago by
yxwucq
• 0
0
votes
1
reply
161
views
Hide positions in alignment with 99% "–" characters to ignore single sequence insertions?
alignment
gaps
updated 2 days ago by
b.contreras.moreira
▴ 170 • written 2 days ago by
Broccoli
• 0
0
votes
1
reply
161
views
Plot DNA methylation level of DMR on the basis of certain genes
rrbs
methylkit
updated 3 days ago by
GenoMax
141k • written 3 days ago by
Srinka
▴ 20
1
vote
1
reply
160
views
WGCNA preservation analysis
WGCNA
preservation
updated 3 days ago by
Michael
54k • written 4 days ago by
michael.flower.14
▴ 180
0
votes
1
reply
156
views
Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering
subclustering
scRNAseq
updated 3 days ago by
bk11
★ 2.4k • written 3 days ago by
alphaflylizard
• 0
0
votes
1
reply
153
views
RNA-seq bacteria contamination
RNA-seq
updated 4 days ago by
GenoMax
141k • written 5 days ago by
sh
• 0
0
votes
1
reply
149
views
How to solve this RoseTTAFold colaboratory error?
modeling
Google
Colaboratory
RoseTTAFold
protein
updated 3 days ago by
Mensur Dlakic
★ 27k • written 3 days ago by
benguyarenbeyaz98
• 0
1
vote
1
reply
147
views
Including plasmid in transcriptome assemblies
Bacteria
BOWTIE2
Transcriptomics
STAR
updated 3 days ago by
GenoMax
141k • written 3 days ago by
heelpPlease
• 0
0
votes
1
reply
146
views
Identification of Transgene insertion sites
Transgene
Whole-Genome-Sequencing
transgene-sites
updated 4 days ago by
Ram
43k • written 4 days ago by
Cameron.walker9900
• 0
0
votes
1
reply
143
views
GEMMA GWAS how to specify factor or numerical for covariates
covariate
GEMMA
GWAS
updated 2 days ago by
Sofia
• 0 • written 2 days ago by
mawigoj318
• 0
0
votes
0
replies
139
views
How to extract the mutations specific to cancer after variant annotation
variant-annotation
updated 5 days ago by
Ram
43k • written 6 days ago by
sainavyav22
• 0
0
votes
1
reply
138
views
Subset Seurat object from Xenium spatial data
Seurat
Xenium
Spatial
updated 3 days ago by
bk11
★ 2.4k • written 4 days ago by
Susmita Mandal
▴ 110
0
votes
0
replies
138
views
Bacterial genome alignment with mauve
Bacteria
mauve
genome
6 days ago by
rthapa
▴ 90
0
votes
1
reply
136
views
Normalize scRNAseq data to housekeeping genes to compare several datasets
RNA-sequencing
housekeeping
Single-cell
normalization
updated 1 day ago by
ATpoint
82k • written 1 day ago by
AaronJaime
• 0
0
votes
1
reply
135
views
tbtool
tbtool
updated 4 days ago by
Ram
43k • written 4 days ago by
Raman
• 0
0
votes
1
reply
134
views
FAM FILE
file
Fam
5 days ago by
Eleonora
• 0
0
votes
0
replies
134
views
Sequence BLAST in plus/minus and plus/plus
blast
CRISPR
strand
sequencing
3 days ago by
salias
• 0
0
votes
0
replies
134
views
Correlation between cell type prediction scores and individual gene expression in spatial transcriptomic datasets
single-cell
Spatial-Transcriptomics
12 hours ago by
biocellbio
• 0
0
votes
0
replies
134
views
Reparametrization of .str (param penalty > 100) File from CGenFF for Ligand Simulation in GROMACS
Simulation
CGenFF
Gromacs
VMD
6 days ago by
Mamatha Y S
• 0
0
votes
1
reply
133
views
Plots for DNA methylation data
plots
DNA
methylation
updated 3 days ago by
GenoMax
141k • written 4 days ago by
sarahawan92
▴ 10
0
votes
0
replies
132
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
TCGA
GDCprepare
updated 2 days ago by
Ram
43k • written 2 days ago by
glaciya2018
• 0
0
votes
0
replies
132
views
News:
upcoming online statistical courses
Statistics
R
Data-Analysis
updated 5 days ago by
Ram
43k • written 6 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
131
views
Can you give me an example of a small globular protein (PDB) that has disordered alpha-carbons?
protein
pdb
alpha-carbon
2 days ago by
4fzcgueyp5
• 0
0
votes
0
replies
129
views
CIRIquant: ValueError: file has no sequences defined (mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False
Ciriquant
updated 5 days ago by
Carlo Yague
8.7k • written 5 days ago by
Atul K.
• 0
0
votes
0
replies
128
views
Job:
Ensembl Plants Senior Bioinformatician
ebi
embl
genomics
ensembl
4 days ago by
Ben_Ensembl
★ 2.4k
0
votes
1
reply
127
views
Displaced fragment length distribution in ATAC-seq
ATAC-seq
nucleosome
fragment
updated 4 days ago by
ATpoint
82k • written 4 days ago by
enanoide
• 0
0
votes
0
replies
125
views
Job:
CTO/founding engineer role at Voyant Bio
engineer
1 day ago by
Assaf
• 0
3
votes
0
replies
118
views
News:
Interested in Spatial Omics?
Bioconductor
Spatial-Omics
Spatial-Transcriptomics
updated 3 days ago by
Ram
43k • written 3 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
115
views
News:
8th Berlin Summer School in NGS Data Analysis - Apply Now
DNA-seq
variant-calling
RNA-seq
illumina
transcriptomics
updated 1 day ago by
Ram
43k • written 2 days ago by
David Langenberger
11k
0
votes
0
replies
115
views
Alternative splicing analysis using SUPPA tool - how to normalise counts?
rna-seq
single-cell
suppa
alternative-splicing
updated 2 days ago by
Ram
43k • written 3 days ago by
newuser2024
• 0
0
votes
0
replies
111
views
News:
hands-on introduction to generalized linear models (GLMs) using R
Generalized-Linear-Models
GLM
R
updated 2 days ago by
Ram
43k • written 3 days ago by
carlopecoraro2
★ 2.5k
1
vote
0
replies
110
views
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
dnds
kaks
VCF
1 day ago by
rohitsatyam102
▴ 850
0
votes
0
replies
109
views
Phasing VCF Files and Analyzing Reads with Multiple Variants
haplotypes
vcf
phasing
1 day ago by
HarperReed
• 0
1
vote
1
reply
109
views
Source other conda environments in a nextflow pipeline when nextflow itself is in a conda environment?
hpc
conda
nextflow
updated 15 hours ago by
ATpoint
82k • written 15 hours ago by
chaco001
▴ 40
3
votes
0
replies
109
views
News:
Webinar “Learning Single-cell Atlases” with Dr. Fabian Theis, author of Scanpy on May 8
Scanpy
Generative-AI
scRNA
Machine-Learning
updated 13 hours ago by
Ram
43k • written 23 hours ago by
Claire Watson
▴ 60
0
votes
0
replies
108
views
Pairwise alignment and Ka/Ks computation
Pairwise-Alignment
Genomics
Ka-Ks
updated 4 days ago by
Ram
43k • written 4 days ago by
maxime.policarpo
▴ 200
0
votes
1
reply
108
views
gvcf joint calling
WES
GATK
VCF
gVCF
updated 1 day ago by
Jeremy Leipzig
22k • written 1 day ago by
zihanss
• 0
183 results • Page
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Answer: Heatmap and rna-seq
Comment: Heatmap and rna-seq
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They say that we remember better things we figured out on our own, rather than things we were taught. You were literally two clicks away fr…
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https://maayanlab.cloud/clustergrammer/ It's a web-based tool (can also be a python jupyter widget) that I find useful for exploring a pat…
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There is an Agilent array case study in the limma User's Guide, which you might find helpful and somewhat simpler. I don't recommend col…
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Thank you Pierre! I'll try this out with my full data set.
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I happend to see one paper doing the similar thing, share it with you guys, "A systematic evaluation of normalization methods and probe rep…
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You need to be clear about how `Seurat` defines highly variable genes here. Highly variable genes are the genes that have very high express…
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Please include a link when you are recommending a tool. There can be programs with similar names.
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Check out clustergrammer from Avi Ma'ayan's lab.
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Simple: ```r data <- lapply(files, read_tsv) data <- Reduce(merge, data) # or Reduce(full_join, data) ``` <a href="" title="Text added bec…
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Hi, Just thought I'd share this code snippet here for when each file contains multiple samples. I tried using lapply (as suggested by Ram)…
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