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36 results • Page
1 of 1
Sort: Votes
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Views
Votes
Replies
3
votes
4
replies
202
views
retaining only the clusters of interest
seurat
single-cell
scRna-seq
updated 1 hour ago by
Ram
39k • written 19 hours ago by
shamza
• 0
2
votes
3
replies
216
views
Same GEO Accession, different SRR number, how to download this RNA-seq paired-end data?
sra-toolkit
fastq
RNA-seq
SRA
updated 23 hours ago by
GenoMax
130k • written 1 day ago by
ev97
• 0
2
votes
2
replies
182
views
bioinformatic analysis protocol performed by CD Genomics
Genomics
analysis
CD
Protocol
updated 22 hours ago by
Ram
39k • written 6 days ago by
linnet.roque6
▴ 10
2
votes
6
replies
646
views
How to identify the corresponding gene of a short sequence of a genome?
fasta
gene
genome
sequence
updated 22 hours ago by
Ram
39k • written 3.5 years ago by
Kumar
▴ 100
1
vote
3
replies
221
views
Differential protein expression analysis
R
proteomic
statistics
updated 2 hours ago by
dsull
★ 4.2k • written 3 days ago by
Ribo
▴ 40
1
vote
2
replies
141
views
phage genome submission in ncbi genebank
phage
table2asn
ncbi
56 minutes ago by
tahsinkhan570
• 0
1
vote
4
replies
71
views
How to use R installed by conda instead of it installed by apt on Ubuntu
R
ubuntu
conda
updated 4 minutes ago by
ATpoint
72k • written 2 hours ago by
Zhichao
• 0
1
vote
1
reply
43
views
switching from illumination to NEB prep kits
NEB
WGS
WES
illumina
updated 1 hour ago by
GenoMax
130k • written 2 hours ago by
lait
▴ 170
1
vote
3
replies
110
views
Masking before RNA-Seq Alignment and Gene Prediction in Plant Genomes
RNA-evidence
genome
prediction
masking
updated 2 hours ago by
Darked89
4.4k • written 5 hours ago by
Ayish
• 0
1
vote
3
replies
598
views
What is the best approach to detect unknown recombinant gene in genome?
recombinant
sequencing
updated 20 hours ago by
Ram
39k • written 3.4 years ago by
Can Holyavkin
▴ 240
0
votes
1
reply
76
views
What is the possibility of Depth (DP) being higher than the coverage
GATK
DP
Coverage
Depth
HaplotypeCaller
updated 8 hours ago by
seidel
11k • written 9 hours ago by
dare_devil
★ 3.1k
0
votes
1
reply
108
views
CIBERSORT Error: File not found
CIBERSORT
updated 7 hours ago by
ATpoint
72k • written 17 hours ago by
jcara514
• 0
0
votes
1
reply
162
views
Information on sequin RNA spike in standards
Sequin
Spike-in
RNA-seq
updated 6 hours ago by
ATpoint
72k • written 1 day ago by
akainth
▴ 10
0
votes
2
replies
146
views
What does "OS_CNSR" and "PFS_CNSR" mean?
survival
cancer
r
5 hours ago by
JACKY
▴ 100
0
votes
2
replies
1.6k
views
How to handle NaN in emmax Kinship matrix?
GWAS
SNP
updated 4 hours ago by
Thu
• 0 • written 5.1 years ago by
CWesse
• 0
0
votes
0
replies
24
views
ERROR: LoadError: UndefVarError: `composition` not defined ?
Protpram
3 hours ago by
Sapphire
• 0
0
votes
1
reply
45
views
DESeq2 for different design and normalized counts
DESeq2
log2foldchange
updated 2 hours ago by
ATpoint
72k • written 2 hours ago by
t.ru
▴ 20
0
votes
0
replies
16
views
Methylation (Illumina arrays or Whole-genome bisulfite sequencing WBS) and WGS datasets?
array
wgs
methylation
wbs
dna
2 hours ago by
cate.cevallos
• 0
0
votes
1
reply
39
views
Alternative To interactions comparison in limma in DESeq2
DESeq2
interactions
updated 2 hours ago by
ATpoint
72k • written 2 hours ago by
f2ff7a46
• 0
0
votes
1
reply
34
views
Visualizing several genomes/plasmids in a single figure
visualization
updated 1 hour ago by
GenoMax
130k • written 2 hours ago by
blur
▴ 270
0
votes
0
replies
14
views
m6A-seq input normalisation with RNA-seq
m6A-seq
MeRIP-Seq
normalisation
deepTools
updated 53 minutes ago by
Ram
39k • written 55 minutes ago by
Pari
• 0
0
votes
0
replies
8
views
TCGA input files for COHCAP
TCGA
methylation
COHCAP
45 minutes ago by
dilrajkaur766
• 0
0
votes
0
replies
36
views
Complex Phylogenetic Tree Annotation
annotation
protein
phylogenetic-tree
updated 34 minutes ago by
Ram
39k • written 4 hours ago by
Aanushka
• 0
0
votes
1
reply
20
views
Is the Kruskal-Wallis test appropriate for genomic distances?
Statistics
Bioinformatics
updated 16 minutes ago by
ATpoint
72k • written 1 hour ago by
aaronlogsdon2001
• 0
0
votes
1
reply
665
views
Is there bioinformatics tool to check cross hybridization between primers and probes?
primer
cross-hybridisation
pcr
updated 6 minutes ago by
Tawny
▴ 180 • written 2.7 years ago by
Pramod Shinde
• 0
0
votes
1
reply
5
views
snps from empty well, Illumina Sequencing
Illumina
SNP
sequencing
updated just now by
GenoMax
130k • written 6 minutes ago by
saint-even
• 0
0
votes
1
reply
4
views
sgRNA design
gene
editing
updated just now by
GenoMax
130k • written 3 minutes ago by
elisa.qinxue
• 0
0
votes
6
replies
332
views
variant allelic fraction
vep
updated 23 hours ago by
Ram
39k • written 2 days ago by
Jom
• 0
0
votes
8
replies
1.5k
views
Chromosome Location of Sequence in Fasta File using Biopython
biopython
python
updated 23 hours ago by
Ram
39k • written 3.5 years ago by
muhammad.khizerkiet
• 0
0
votes
0
replies
368
views
How to compile Java files in bash?
Bash
Java
updated 22 hours ago by
Ram
39k • written 19 months ago by
ezraamustafa3
• 0
0
votes
2
replies
770
views
Error in mvnX when running processSamples.R of OncoCNV
variant-calling
oncocnv
cnv
updated 22 hours ago by
Ram
39k • written 3.5 years ago by
mwarrier
• 0
0
votes
4
replies
652
views
Error in PGAP pangenome pipeline?
sequence
genome
sequencing
gene
updated 20 hours ago by
Ram
39k • written 3.5 years ago by
Kumar
▴ 100
0
votes
0
replies
480
views
selection analysis of non coding sequences
hyphy
selection-analysis
updated 20 hours ago by
Ram
39k • written 3.5 years ago by
vafamayahi
• 0
0
votes
0
replies
588
views
Taxonomy from Pfam database
taxonomy
pfam
updated 20 hours ago by
Ram
39k • written 3.5 years ago by
shibl_a
▴ 20
0
votes
2
replies
189
views
Correct way to remove Nextera adapters from ITS sequences
adapters
ITS
trimmomatic
16 hours ago by
mattze731
▴ 10
0
votes
3
replies
222
views
Gviz Coverage Plots
gviz
scrnaseq
cellranger
r
updated 15 hours ago by
Ram
39k • written 21 hours ago by
Researcher
• 0
36 results • Page
1 of 1
Recent Votes
Answer: Limma returned only positive logFC values
Answer: Limma returned only positive logFC values
Comment: How to use R installed by conda instead of it installed by apt on Ubuntu
Comment: ChatGPT optimized for bioinformatics questions
ChatGPT optimized for bioinformatics questions
The Biostar Herald for Monday, June 05, 2023
Comment: switching from illumination to NEB prep kits
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▴ 260
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▴ 170
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130k
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Recent Replies
Answer: counts matrix should be numeric, currently it has mode: character when using a c
by
ATpoint
72k
You have commas as decimal delimiters which interpreted as text. Just replace by dot and make numeric: ```r d <- data.frame(A=c("1,2", "3,…
Comment: sgRNA design
by
GenoMax
130k
Library fragments can be in forward/reverse orientation (w.r.t reference sequence) so it is possible to see sequence from either strand in …
Comment: snps from empty well, Illumina Sequencing
by
GenoMax
130k
> I receive illumina sequencing files with 96 wells, our lab leaves one > well empty. When I process the files with a SNP calling pipeline …
Answer: counts matrix should be numeric, currently it has mode: character when using a c
by
Darked89
4.4k
You can try: counts_data <- read.csv2("normalized.csv", header = TRUE) But as far as I know DESeq2 requires raw counts as inpu…
Comment: Is there bioinformatics tool to check cross hybridization between primers and pr
by
Tawny
▴ 180
Was a tool ever found for this? I am curious.
Comment: Is the Kruskal-Wallis test appropriate for genomic distances?
by
ATpoint
72k
I never used it myself so far, but I would proably look into https://bioconductor.org/packages/devel/bioc/vignettes/nullranges/inst/doc/nul…
Comment: ChatGPT optimized for bioinformatics questions
by
GenoMax
130k
Since you have kept the bot openly accessible (at least for now) this is great. People can try it out and hopefully provide feedback. I tri…
Comment: How to use R installed by conda instead of it installed by apt on Ubuntu
by
jv
★ 1.2k
if you are doing these steps then the `R` version should be `4.1.1`. Are you sure there weren't any errors during the install of `r-base=4.…
Comment: How to use R installed by conda instead of it installed by apt on Ubuntu
by
Ram
39k
Please follow this sequence of steps and show us the outputs: ``` # Start from a fresh terminal with no conda environment active: which -a…
Comment: ChatGPT optimized for bioinformatics questions
by
Ram
39k
Happy to help!
Comment: phage genome submission in ncbi genebank
by
tahsinkhan570
• 0
Thanks for the info. I called the --compliant and later removed the Ec_number of hypothetical protein as mentioned by NCBI table2asn guidel…
Comment: ChatGPT optimized for bioinformatics questions
by
Sasha
▴ 260
Great use case - we'll take a look. Thanks for trying it out!
Comment: retaining only the clusters of interest
by
Ram
39k
You're close. The `subset` function serves a similar functionality as the base, but since the Seurat object is an S3 object, it subsets bas…
Answer: ChatGPT optimized for bioinformatics questions
by
Ram
39k
I asked the same questions to tinyBio and chatGPT and chatGPT gave me better answers. This could be because chatGPT has been out for a whil…
Comment: ChatGPT optimized for bioinformatics questions
by
Sasha
▴ 260
Hi GenoMax - it's primed on Github repos, some personality tuning, and some prompt assumptions based on the context of the site being bioin…
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