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1,000 results • Page
1 of 20
Sort: Views
Rank
Views
Votes
Replies
226
votes
39
replies
281k
views
33 follow
Gene Id Conversion Tool
mapping
conversion
updated 7 months ago by
Ram
38k • written 13.4 years ago by
Renee
▴ 620
64
votes
3
replies
268k
views
Understanding up and down regulated genes from LOG2 foldchange or foldchange
protein
gene-expression
RNA-Seq
updated 17 days ago by
Ram
38k • written 8.8 years ago by
Whoknows
▴ 960
267
votes
29
replies
251k
views
25 follow
How To Filter Mapped Reads With Samtools
samtools
updated 4 months ago by
Ram
38k • written 10.4 years ago by
sohadb1357
▴ 610
319
votes
90
replies
214k
views
57 follow
Tools To Calculate Average Coverage For A Bam File?
coverage
bam
sequencing
updated 6 months ago by
Ram
38k • written 12.2 years ago by
Biomed
4.8k
43
votes
24
replies
193k
views
25 follow
How To Update R In Ubuntu ?
r
ubuntu
updated 11 months ago by
matthew.pace
▴ 50 • written 9.3 years ago by
Arpitha Hebbar
▴ 210
151
votes
42
replies
174k
views
22 follow
How Do I Draw A Heatmap In R With Both A Color Key And Multiple Color Side Bars?
heatmap
r
updated 10 months ago by
Ram
38k • written 11.1 years ago by
Obi Griffith
20k
276
votes
39
replies
164k
views
29 follow
Tutorial:
How to download raw sequence data from GEO/SRA
fastq
SRA
download
GEO
bam
updated 10 months ago by
Ram
38k • written 8.6 years ago by
Obi Griffith
20k
188
votes
21
replies
163k
views
11 follow
Forward And Reverse Strand Conventions
sequence
strand
updated 4 months ago by
Istvan Albert
97k • written 12.4 years ago by
Andrea_Bio
★ 2.8k
133
votes
18
replies
154k
views
16 follow
Blast - Formatting Output
blast
format
output
updated 3 months ago by
katieostrouchov
▴ 20 • written 9.3 years ago by
timjoncooper
▴ 310
158
votes
8
replies
150k
views
Generate vcf.gz file and its index file vcf.gz.tbi
vcf
tabix
updated 8 months ago by
Ram
38k • written 10.3 years ago by
lyz10302012
▴ 430
358
votes
79
replies
136k
views
34 follow
Tool:
Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
parallel
next-gen
ngs
updated 4 months ago by
Ram
38k • written 10.1 years ago by
ole.tange
★ 4.3k
223
votes
38
replies
134k
views
29 follow
Tool:
Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
genome
coordinates
conversion
liftover
ensembl
Tool
updated 3 months ago by
harelarik
▴ 90 • written 10.1 years ago by
Malachi Griffith
19k
90
votes
38
replies
128k
views
18 follow
Extract Reads From A Bam File That Fall Within A Given Region
bam
updated 6 months ago by
Wang Cong
▴ 10 • written 10.7 years ago by
abi
▴ 370
143
votes
30
replies
126k
views
25 follow
Useful Bash Commands To Handle Fasta Files
command-line
command-line
fasta
list
bash
updated 6 months ago by
Ram
38k • written 11.1 years ago by
Anima Mundi
★ 2.9k
129
votes
32
replies
122k
views
29 follow
Is There A Free Alternative To Ingenuity Pathway Analysis?
network
pathway
updated 11 months ago by
Ram
38k • written 12.0 years ago by
Gon
▴ 530
23
votes
9
replies
121k
views
8 follow
How to calculate "fold changes" in gene expression?
R
gene
updated 6 weeks ago by
Ram
38k • written 7.9 years ago by
juan.rosas1
▴ 70
26
votes
10
replies
120k
views
Calculating P-Values From Z-Scores
statistics
r
updated 9 months ago by
Ram
38k • written 11.1 years ago by
Diana
▴ 900
13
votes
8
replies
118k
views
7 follow
Convert A Text File Into A Fasta File
fasta
updated 5 months ago by
Ram
38k • written 11.4 years ago by
Zhshqzyc
▴ 500
97
votes
9
replies
113k
views
11 follow
How To Merge Two Fastq.Gz Files?
merge
fastq
updated 11 months ago by
henry-keen
▴ 40 • written 9.5 years ago by
newDNASeqer
▴ 750
46
votes
10
replies
112k
views
8 follow
Which Expression Units To Use, Fpkm Or Rpkm ?
fpkm
rpkm
rna-seq
updated 3 months ago by
Ram
38k • written 10.0 years ago by
biorepine
★ 1.5k
729
votes
161
replies
108k
views
100 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 9 days ago by
Biostar
1.6k • written 6.3 years ago by
Istvan Albert
97k
73
votes
25
replies
97k
views
14 follow
How to count fastq reads
sequence
next-gen
fastq
reads
updated 8 months ago by
Ram
38k • written 7.9 years ago by
Chenglin
▴ 250
100
votes
15
replies
97k
views
15 follow
Convertion Of Gff3 To Gtf
gtf
gff
updated 19 days ago by
Genetics
▴ 20 • written 10.8 years ago by
GouthamAtla
12k
59
votes
9
replies
94k
views
10 follow
Blog:
Gene expression units explained: RPM, RPKM, FPKM and TPM
gene-expression
RNA-Seq
updated 6 weeks ago by
Ram
38k • written 5.5 years ago by
Renesh
★ 2.1k
274
votes
33
replies
92k
views
25 follow
Tutorial:
Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates
updated 22 days ago by
Ram
38k • written 9.4 years ago by
Obi Griffith
20k
118
votes
53
replies
87k
views
22 follow
How to plot coverage and depth statistics of a bam file
bam
coverage
depth
next-gen-sequencing
updated 4 days ago by
Raag
• 0 • written 8.8 years ago by
kay
▴ 330
97
votes
19
replies
87k
views
12 follow
How To Get The Sequence Of A Genomic Region From Ucsc?
sequence
ucsc
fasta
updated 7 months ago by
Ram
38k • written 13.1 years ago by
Giovanni M Dall'Olio
27k
70
votes
16
replies
85k
views
12 follow
What Does Samtools Flagstat Results Mean?
rna
samtools
mouse
updated 11 months ago by
Pierre Lindenbaum
153k • written 11.5 years ago by
Sakti
▴ 510
167
votes
41
replies
85k
views
27 follow
Multiline Fasta To Single Line Fasta
sequence
fasta
updated 7 weeks ago by
Onur
• 0 • written 11.8 years ago by
Palu
▴ 240
238
votes
176
replies
84k
views
73 follow
Tutorial:
Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq
Survival
TCGA
updated 5 months ago by
Ram
38k • written 7.6 years ago by
TriS
★ 4.6k
84
votes
16
replies
84k
views
9 follow
Number of mapped reads from BAM file
bam
sam
reads
mapping
updated 4 months ago by
bhanu.chandra1
▴ 50 • written 7.9 years ago by
Prakki Rama
★ 2.6k
99
votes
31
replies
81k
views
18 follow
Best Way To Merge A Many Thousand Small Bam Files Into One Big Bam File?
bam
picard
samtools
merge
updated 8 months ago by
Ram
38k • written 11.7 years ago by
2184687-1231-83-
★ 5.0k
79
votes
22
replies
81k
views
16 follow
How To Split One Big Sequence File Into Multiple Files With Less Than 1000 Sequences In A Single File
next-gen
sequencing
fasta
rna
r
perl
updated 4 months ago by
Ram
38k • written 11.4 years ago by
Hamilton
▴ 290
106
votes
45
replies
80k
views
30 follow
How To Extract A Sequence From A Big (6Gb) Multifasta File ?
fasta
updated 6 months ago by
aswinssoman
▴ 20 • written 10.7 years ago by
Mchimich
▴ 320
70
votes
20
replies
80k
views
15 follow
How To Get Ensembl Id (Gene, Transcript, Protein) Mapping Information?
ensembl
identifiers
mapping
updated 10 weeks ago by
Ram
38k • written 12.4 years ago by
Unode
▴ 180
55
votes
11
replies
79k
views
8 follow
merge large amount of fastq files into a single one
ChIP-Seq
fastq
updated 9 months ago by
Ram
38k • written 8.0 years ago by
catherine
▴ 220
185
votes
43
replies
78k
views
29 follow
Drawing Chromosome Ideograms With Data
chromosome
visualization
ideogram
updated 6 months ago by
Ram
38k • written 13.0 years ago by
Yuri
★ 1.6k
136
votes
25
replies
75k
views
14 follow
Tutorial:
Piping With Samtools, Bwa And Bedtools
unix
samtools
bwa
bedtools
updated 11 months ago by
Ram
38k • written 10.9 years ago by
Ying W
★ 4.2k
157
votes
62
replies
74k
views
37 follow
Selecting Random Pairs From Fastq?
random
fastq
sequence
illumina
code
updated 9 months ago by
erin.baschal
• 0 • written 12.0 years ago by
Ketil
4.1k
94
votes
25
replies
74k
views
20 follow
Extract Sub-Set Of Regions From Vcf File
vcf
tabix
genome
filter
updated 10 days ago by
4galaxy77
2.6k • written 10.8 years ago by
Rubal7
▴ 820
15
votes
12
replies
73k
views
8 follow
BLAST Database error: No alias or index file found for nucleotide database
blast
blastn
sift
makeblastdb
updated 7 months ago by
Luke
• 0 • written 8.4 years ago by
arronslacey
▴ 310
103
votes
12
replies
71k
views
7 follow
Bedtools Compare Multiple Bed Files?
bedtools
intersect
updated 5 months ago by
Ram
38k • written 11.4 years ago by
Bioscientist
★ 1.7k
81
votes
21
replies
71k
views
13 follow
Tutorial:
How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools
samtools
htslib
updated 5 weeks ago by
cmdcolin
★ 2.9k • written 4.7 years ago by
otwtgin2010
▴ 530
67
votes
18
replies
69k
views
17 follow
Project For A Beginner Bioinformatics Student
project
java
updated 8 months ago by
Ram
38k • written 11.4 years ago by
And
▴ 230
33
votes
17
replies
69k
views
14 follow
How To Draw A Heat Map For Gene Expression Data?
microarray
heatmap
updated 9 weeks ago by
Ram
38k • written 11.8 years ago by
Fahmida
▴ 80
40
votes
14
replies
68k
views
9 follow
Synonymous And Non-Synonymous Snps
snp
updated 10 months ago by
Ram
38k • written 12.2 years ago by
Elena
▴ 250
194
votes
44
replies
68k
views
33 follow
Tutorial:
Analysing Microarray Data In Bioconductor
microarray-analysis
bioconductor
updated 10 weeks ago by
Ram
38k • written 10.5 years ago by
Obi Griffith
20k
188
votes
50
replies
67k
views
41 follow
How To Remove The Same Sequences In The Fasta Files?
fasta
sequence
duplicates
updated 5 months ago by
Ram
38k • written 12.4 years ago by
Zhangleisdau
▴ 340
59
votes
15
replies
67k
views
9 follow
BAM/SAM to FASTA conversion
sam
bam
updated 11 months ago by
Ram
38k • written 8.1 years ago by
biolab
★ 1.4k
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 9.3 years ago by
Nicholas Spies
★ 1.2k
1,000 results • Page
1 of 20
Recent Votes
Comment: bioinformatics problems solved by graphs data structure
Comment: bioinformatics problems solved by graphs data structure
Answer: How to analize multiple letters codes in COG IDs?
Answer: PCA in gene expression
Answer: PCA in gene expression
Comment: Enrichment analysis based on kegg for zebrafish
Question on number of possible alignments
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Comment: bioinformatics problems solved by graphs data structure
by
lieven.sterck
14k
et mon français est assez bien pour comprendre ce que tu as écrit la ;-)
Comment: How to analize multiple letters codes in COG IDs?
by
Constanza
• 0
Thanks for answering so fast, it was very helpful. I shouldn't pay much attention to if COGs are separated by a comma or not then. As long…
Comment: bioinformatics problems solved by graphs data structure
by
lieven.sterck
14k
well, because this is not you guys' private forum, there are other people participating (not native french speaking) , just to give a reaso…
Answer: How to get gene from PSIBLAST resuts
by
lieven.sterck
14k
what you likely will need to do: 1. get the ID of the protein that you are interested in (out of result from PSIBLAST) 2. lookup that ID…
Answer: How to analize multiple letters codes in COG IDs?
by
Mensur Dlakic
★ 23k
The meaning of individual letters is described in a well-known COG functional code: https://ecoliwiki.org/colipedia/index.php/Clusters_o…
Comment: How to find promoter sequence of a gene?
by
sunyeping
▴ 40
The organism is mice.
Answer: How to generate GFF/GTF file from cDNA transcipts FASTA file?
by
Pierre Lindenbaum
153k
BLAT your cDNAs to the reference. This should be a PSL file that can be converted to a psl->gff3 converter (e.g: https://github.com/gperte…
Comment: RNAseq: same reads + more complete scaffold = fewer DEGs?
by
Darked89
4.2k
You may try to check what happened with DEGs obtained using the 300 fragments assembly by getting the sequences of these genes and comparin…
Comment: ExomeDepth installation error
by
Medha
• 0
Thanks, that did work. Also in next steps, there are some arguments like bam.files, I was wondering do we require to have multiple bam fil…
Comment: ExomeDepth installation error
by
jared.andrews07
★ 14k
No idea, I don't use databricks. I'd read the docs, find a local expert to help you out, or contact their support, likely in that order.
Comment: ExomeDepth installation error
by
Medha
• 0
Hi @jaredandrews07 thanks for reverting back. I am new to R and just want to make sure ExomeDepth is working for the first time. For the Rs…
Comment: Embedded stop codon in translated nucleotide sequences in DAMBE
by
Mensur Dlakic
★ 23k
It is not obvious to me what exact steps you did here, but here is what I do know: there will always be stop codons even in open reading fr…
Comment: Error with a function in ATAC-seq analysis
by
Chris
▴ 70
So you skip the GRanges()? Yes, no error anymore but I am not sure if that causes changing in downstream analysis.
Answer: ClusterProfiler enrichKEGG – remove organism name in plots?
by
jv
★ 1.0k
`stringr::str_remove` can remove " - Mus musculus (house mouse)" from the pathway names which are stored under `KEGGPATHID2NAME$to` in your…
Comment: Error with a function in ATAC-seq analysis
by
jv
★ 1.0k
run `union` on the data frames
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